ClinVar Genomic variation as it relates to human health
NM_017739.4(POMGNT1):c.1895+1G>T
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_017739.4(POMGNT1):c.1895+1G>T
Variation ID: 56593 Accession: VCV000056593.34
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 1p34.1 1: 46189457 (GRCh38) [ NCBI UCSC ] 1: 46655129 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
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First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Jul 24, 2013 Jun 17, 2024 Mar 18, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_017739.4:c.1895+1G>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
splice donor NM_001243766.2:c.1869+27G>T intron variant NM_001290129.2:c.1829+1G>T splice donor NM_001290130.2:c.1466+1G>T splice donor NM_001410783.1:c.1895+1G>T splice donor NC_000001.11:g.46189457C>A NC_000001.10:g.46655129C>A NG_009205.3:g.35849G>T LRG_701:g.35849G>T LRG_701t1:c.1869+27G>T LRG_701t2:c.1895+1G>T - Protein change
- Other names
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- Canonical SPDI
- NC_000001.11:46189456:C:A
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
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Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
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Allele frequency
Help
The frequency of the allele represented by this VCV record.
The Genome Aggregation Database (gnomAD) 0.00009
Exome Aggregation Consortium (ExAC) 0.00011
Trans-Omics for Precision Medicine (TOPMed) 0.00012
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
Help
Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
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HI score
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The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
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The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
Help
The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
Help
The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
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POMGNT1 | - | - |
GRCh38 GRCh37 |
260 | 1423 | |
TSPAN1 | - | - |
GRCh38 GRCh37 |
15 | 1154 |
Conditions - Germline
Condition
Help
The condition for this variant-condition (RCV) record in ClinVar. |
Classification
Help
The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
Help
The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
Help
The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
Help
The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
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Pathogenic/Likely pathogenic (2) |
no assertion criteria provided
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Sep 16, 2020 | RCV000050006.11 | |
Pathogenic (2) |
criteria provided, multiple submitters, no conflicts
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Mar 8, 2022 | RCV000490077.15 | |
Pathogenic (1) |
criteria provided, single submitter
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Jan 28, 2024 | RCV000704718.13 | |
Pathogenic (2) |
criteria provided, multiple submitters, no conflicts
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Feb 14, 2024 | RCV000778243.12 | |
Pathogenic (2) |
criteria provided, multiple submitters, no conflicts
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Aug 21, 2019 | RCV001005010.11 | |
Pathogenic (1) |
criteria provided, single submitter
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Jul 2, 2018 | RCV001266790.9 | |
Pathogenic (2) |
criteria provided, multiple submitters, no conflicts
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Mar 18, 2024 | RCV001810416.12 | |
Pathogenic (1) |
criteria provided, single submitter
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Oct 19, 2020 | RCV002470741.8 | |
Likely pathogenic (1) |
criteria provided, single submitter
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Jan 24, 2023 | RCV002513698.10 |
Submissions - Germline
Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
Help
The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
Help
The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
Help
This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
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Pathogenic
(May 03, 2018)
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criteria provided, single submitter
Method: clinical testing
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POMGNT1-Related Disorders
Affected status: unknown
Allele origin:
germline
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Illumina Laboratory Services, Illumina
Accession: SCV000914412.1
First in ClinVar: May 27, 2019 Last updated: May 27, 2019 |
Comment:
The POMGNT1 c.1895+1G>T variant occurs in a canonical splice site (donor) and is therefore predicted to disrupt or distort the normal gene product. The variant … (more)
The POMGNT1 c.1895+1G>T variant occurs in a canonical splice site (donor) and is therefore predicted to disrupt or distort the normal gene product. The variant has been reported in at least four studies in which it is found in a compound heterozygous state in three individuals with muscle-eye-brain disease and in one individual with cobblestone lissencephaly (Diesen et al. 2004; Mercuri et al. 2009; Saredi et al. 2012; Devisme et al. 2012). The variant was absent from at least 125 control individuals and is reported at a frequency of 0.00047 in the European (non-Finnish) population of the Exome Aggregation Consortium. RT-PCR experiments demonstrated that the variant affects splicing with retention of the intron between exons 21 and 22 (Saredi et al. 2012). Due to the potential impact of splice donor variants and the evidence from the literature, the c.1895+1G>T variant is classified as pathogenic for POMGNT1-related disorders. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. (less)
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Pathogenic
(Dec 03, 2018)
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criteria provided, single submitter
Method: research
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Autosomal recessive limb-girdle muscular dystrophy type 2O
(Autosomal recessive inheritance)
Affected status: yes
Allele origin:
germline
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Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard
Accession: SCV001164571.1
First in ClinVar: Mar 01, 2020 Last updated: Mar 01, 2020 |
Comment:
The homozygous c.1895+1G>T variant in POMGNT1 was identified by our study in one individual with limb-girdle muscular dystrophy (LGMD). This variant has been identified in … (more)
The homozygous c.1895+1G>T variant in POMGNT1 was identified by our study in one individual with limb-girdle muscular dystrophy (LGMD). This variant has been identified in 0.007982% (22/275604) of chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs386834024). Although this variant has been seen in the general population, its frequency is low enough to be consistent with a recessive carrier frequency. This variant occurs in the invariant region (+/- 1/2) of the splice consensus sequence and is predicted to cause altered splicing leading to an abnormal or absent protein. In vitro functional studies provide some evidence that the c.1895+1G>T variant may impact protein function with abnormal splicing and reduced translation (PMID: 22554691). However, these types of assays may not accurately represent biological function. This variant has been observed in the compound heterozygous state, with two variants not reported in ClinVar, in 2 individuals with LGMD as reported by the literature (PMID: 22554691, 22323514). The presence of this variant in combination with a reported pathogenic variant and in an individual with LGMD increases the likelihood that the c.1895+1G>T variant is pathogenic. In summary, this variant meets criteria to be classified as pathogenic for LGMD in an autosomal recessive manner based on the predicted impact of the variant and multiple occurrences reported in the literature in individuals with LGMD. ACMG/AMP Criteria applied: PM2, PVS1, PS3 (Richards 2015). (less)
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Pathogenic
(Oct 27, 2021)
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criteria provided, single submitter
Method: clinical testing
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Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A3
Affected status: unknown
Allele origin:
unknown
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Myriad Genetics, Inc.
Accession: SCV002060325.2
First in ClinVar: Jan 15, 2022 Last updated: Nov 29, 2022 |
Comment:
NM_017739.3(POMGNT1):c.1895+1G>T is a canonical splice variant classified as pathogenic in the context of muscle-eye-brain disease. c.1895+1G>T has been observed in cases with relevant disease (PMID: … (more)
NM_017739.3(POMGNT1):c.1895+1G>T is a canonical splice variant classified as pathogenic in the context of muscle-eye-brain disease. c.1895+1G>T has been observed in cases with relevant disease (PMID: 15466003, 19299310, 22323514, 28688748, 22554691). Functional assessments of this variant are available in the literature (PMID: 22554691). c.1895+1G>T has been observed in population frequency databases (gnomAD: FIN 0.02%). In summary, NM_017739.3(POMGNT1):c.1895+1G>T is a canonical splice variant that has been observed more frequently in cases with the relevant disease than in healthy populations. Please note: this variant was assessed in the context of healthy population screening. (less)
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Pathogenic
(Oct 19, 2020)
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criteria provided, single submitter
Method: clinical testing
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Myopathy caused by variation in POMGNT1
(Autosomal recessive inheritance)
Affected status: yes
Allele origin:
germline
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Victorian Clinical Genetics Services, Murdoch Childrens Research Institute
Additional submitter:
Shariant Australia, Australian Genomics
Accession: SCV002767662.1
First in ClinVar: Dec 24, 2022 Last updated: Dec 24, 2022 |
Comment:
Based on the classification scheme VCGS_Germline_v1.3.3, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism … (more)
Based on the classification scheme VCGS_Germline_v1.3.3, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with POMGNT-related disorders. (I) 0106 - This gene is associated with autosomal recessive disease. (I) 0205 - Variant is predicted to result in a truncated protein (premature termination codon is NOT located at least 54 nucleotides upstream of the final exon-exon junction) with less than 1/3 of the protein sequence affected. (SP) 0210 - Splice site variant proven to affect splicing of the transcript with a known effect on protein sequence. This variant has been shown to result in intron 21 retention and a premature termination codon (PMID: 22554691; 28424332) (SP) 0251 - This variant is heterozygous. (I) 0304 - Variant is present in gnomAD <0.01 for a recessive condition (v2: 22 heterozygotes, 0 homozygotes). (SP) 0309 - An alternative nucleotide change at the same position has been observed in gnomAD (v2: 2 heterozygotes, 0 homozygotes). (I) 0505 - Abnormal splicing is predicted by in silico tools and affected nucleotide is highly conserved. (SP) 0702 - Other canonical splice variants comparable to the one identified in this case have strong previous evidence for pathogenicity (ClinVar; PMID: 26908613). (SP) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals with POMGNT1-related disorders (ClinVar; PMID: 22323514, 15466003, 28688748, 29555514, 28424332, 22554691) (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign (less)
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Pathogenic
(Jul 02, 2018)
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criteria provided, single submitter
Method: clinical testing
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Inborn genetic diseases
Affected status: yes
Allele origin:
germline
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Ambry Genetics
Accession: SCV001444969.2
First in ClinVar: Nov 21, 2020 Last updated: Jan 07, 2023 |
Number of individuals with the variant: 1
Clinical Features:
Hydrocephalus (present) , Feeding difficulties (present) , Optic nerve hypoplasia (present) , Macrocephalus (present) , Prominent forehead (present) , Nystagmus (present) , Severe global developmental … (more)
Hydrocephalus (present) , Feeding difficulties (present) , Optic nerve hypoplasia (present) , Macrocephalus (present) , Prominent forehead (present) , Nystagmus (present) , Severe global developmental delay (present) , Short stature (present) , Midface retrusion (present) , Short nose (present) , Muscular hypotonia (present) (less)
Sex: male
Ethnicity/Population group: Caucasian/Native American
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Likely pathogenic
(Jan 24, 2023)
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criteria provided, single submitter
Method: curation
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Muscular dystrophy-dystroglycanopathy
(Autosomal recessive inheritance)
Affected status: unknown
Allele origin:
germline
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Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard
Accession: SCV003761147.1
First in ClinVar: Feb 07, 2023 Last updated: Feb 07, 2023 |
Comment:
The c.1895+1G>T variant in POMGNT1 has been previously reported in eight individuals with muscular dystrophy-dystroglycanopathy (PMID: 32115343, PMID: 29555514, PMID: 28688748, PMID: 22323514, PMID: 19299310, … (more)
The c.1895+1G>T variant in POMGNT1 has been previously reported in eight individuals with muscular dystrophy-dystroglycanopathy (PMID: 32115343, PMID: 29555514, PMID: 28688748, PMID: 22323514, PMID: 19299310, PMID: 15466003, PMID: 22554691, PMID: 28424332), and has been identified in 0.012% (15/128292) non-Finnish European chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP ID: rs386834024). Although this variant has been seen in the general population in a heterozygous state, its frequency is not high enough to rule out a pathogenic role. This variant has also been reported in ClinVar (Variation ID#:56593) and has been interpreted as pathogenic by Illumina (most recent interpretation; previously interpreted as VUS [2016] and likely pathogenic [2016]), Ambry Genetics, Centre for Mendelian Genomics,University Medical Centre Ljubljana, Broad Institute Rare Disease Group,GeneDx, Invitae, Juha Muilu Group; Institute for Molecular Medicine Finland (FIMM), Myriad Women's Health, Inc., Natera, Inc, PerkinElmer Genomics, and Counsyl. Of these eight affected individuals, one was a compound heterozygote who carried a pathogenic variant with unknown phase (PMID: 29555514) and one was a compound heterozygote who carried a likely pathogenic variant with unknown phase (PMID: 22323514), which increases the likelihood that the c.1895+1G>T variant is pathogenic. The variant was shown by RT-PCR analysis (PMID: 22554691) and muscle RNAseq of patient tissue (PMID: 28424332) to alter splicing and lead to intron retention between exons 21 and 22. This variant is located in the 5’ splice region. Computational tools predict a splicing impact, though this information is not predictive enough to determine pathogenicity. Loss of function of the POMGNT1 gene is an established disease mechanism in autosomal recessive POMGNT1-associated muscular dystrophy-dystroglycanopathy. In summary, although additional studies are required to fully establish its clinical significance, this variant is likely pathogenic for POMGNT1-associated muscular dystrophy-dystroglycanopathy. ACMG/AMP Criteria applied: PVS1_Moderate, PS3, PM3 (Richards 2015). (less)
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Pathogenic
(Mar 22, 2020)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
germline
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Revvity Omics, Revvity
Accession: SCV002019481.3
First in ClinVar: Nov 29, 2021 Last updated: Feb 04, 2024 |
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Pathogenic
(Jan 28, 2024)
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criteria provided, single submitter
Method: clinical testing
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Autosomal recessive limb-girdle muscular dystrophy type 2O
Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B3
Explanation for multiple conditions: Uncertain.
The variant was classified for several related diseases, possibly a spectrum of disease; the variant may be associated with one or more the diseases.
Affected status: unknown
Allele origin:
germline
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Invitae
Accession: SCV000833678.6
First in ClinVar: Oct 10, 2018 Last updated: Feb 28, 2024 |
Comment:
This sequence change affects a donor splice site in intron 21 of the POMGNT1 gene. RNA analysis indicates that disruption of this splice site induces … (more)
This sequence change affects a donor splice site in intron 21 of the POMGNT1 gene. RNA analysis indicates that disruption of this splice site induces altered splicing and likely disrupts the C-terminus of the protein. This variant is present in population databases (rs386834024, gnomAD 0.02%). Disruption of this splice site has been observed in individual(s) with muscular dystrophy-dystroglycanopathy (PMID: 15466003, 22554691, 28424332). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 56593). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that disruption of this splice site results in partial inclusion of intron 21 (also known as intron 25) and introduces a new termination codon (PMID: 28424332). However the mRNA is not expected to undergo nonsense-mediated decay. For these reasons, this variant has been classified as Pathogenic. (less)
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Pathogenic
(Feb 14, 2024)
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criteria provided, single submitter
Method: clinical testing
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POMGNT1-related condition
Affected status: unknown
Allele origin:
germline
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PreventionGenetics, part of Exact Sciences
Accession: SCV004741883.1
First in ClinVar: Mar 16, 2024 Last updated: Mar 16, 2024 |
Comment:
The POMGNT1 c.1895+1G>T variant is predicted to disrupt the GT donor site and interfere with normal splicing. This variant has been reported in several unrelated … (more)
The POMGNT1 c.1895+1G>T variant is predicted to disrupt the GT donor site and interfere with normal splicing. This variant has been reported in several unrelated individuals with muscle-eye-brain disease (see for example, Saredi et al. 2012. PubMed ID: 22554691; Diesen et al. 2004. PubMed ID: 15466003). Functional RNA studies on this variant have shown it leads to retention of intron 21 (Saredi et al. 2012. PubMed ID: 22554691). This variant is reported in 0.020% of alleles in individuals of European (Finnish) descent in gnomAD. Variants that disrupt the consensus splice donor site in POMGNT1 are expected to be pathogenic. This variant is interpreted as pathogenic. (less)
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Pathogenic
(Mar 18, 2024)
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criteria provided, single submitter
Method: clinical testing
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Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A3
Affected status: unknown
Allele origin:
unknown
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Baylor Genetics
Accession: SCV004205952.2
First in ClinVar: Dec 30, 2023 Last updated: Jun 17, 2024 |
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Pathogenic
(Aug 21, 2019)
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criteria provided, single submitter
Method: clinical testing
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Autosomal recessive limb-girdle muscular dystrophy type 2O
Affected status: yes
Allele origin:
unknown
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Centre for Mendelian Genomics, University Medical Centre Ljubljana
Accession: SCV001368122.2
First in ClinVar: Jul 04, 2020 Last updated: Dec 12, 2020 |
Comment:
This variant was classified as: Pathogenic. The following ACMG criteria were applied in classifying this variant: PVS1,PS1.
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Pathogenic
(Mar 08, 2022)
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criteria provided, single submitter
Method: clinical testing
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Not Provided
Affected status: yes
Allele origin:
germline
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GeneDx
Accession: SCV000577451.7
First in ClinVar: May 22, 2017 Last updated: Mar 04, 2023 |
Comment:
Previously reported in individuals with POMGNT1-related disorders who harbor an additional POMGNT1 variant referred for genetic testing at GeneDx and in published literature (Diesen et … (more)
Previously reported in individuals with POMGNT1-related disorders who harbor an additional POMGNT1 variant referred for genetic testing at GeneDx and in published literature (Diesen et al., 2004; Devisme et al., 2012; Saredi et al., 2012); Published functional studies demonstrate the splice defect leads to retention of intron 21 (Saredi et al., 2012); Canonical splice site variant predicted to result in a null allele in a gene for which loss-of-function is a known mechanism of disease; This variant is associated with the following publications: (PMID: 29555514, 32115343, 22554691, 25525159, 17906881, 15466003, 19299310, 22323514, 28424332) (less)
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probable-pathogenic
(-)
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no assertion criteria provided
Method: not provided
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Muscle eye brain disease
Affected status: not provided
Allele origin:
not provided
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Juha Muilu Group; Institute for Molecular Medicine Finland (FIMM)
Accession: SCV000082415.1
First in ClinVar: Jul 24, 2013 Last updated: Jul 24, 2013
Comment:
FinDis database variant: This variant was not found or characterized by our laboratory, data were collected from public sources: see reference
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Comment:
Converted during submission to Likely pathogenic.
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Pathogenic
(Sep 16, 2020)
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no assertion criteria provided
Method: clinical testing
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Muscle-eye-brain disease
Affected status: unknown
Allele origin:
germline
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Natera, Inc.
Accession: SCV001460152.1
First in ClinVar: Jan 02, 2021 Last updated: Jan 02, 2021 |
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Germline Functional Evidence
There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar. |
Citations for germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
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Congenital muscular dystrophy-dystroglycanopathy, type A, featuring bilateral retinal dysplasia and vertical angle kappa. | Peiris TJ | Journal of AAPOS : the official publication of the American Association for Pediatric Ophthalmology and Strabismus | 2018 | PMID: 29555514 |
Congenital muscular dystrophies in the UK population: Clinical and molecular spectrum of a large cohort diagnosed over a 12-year period. | Sframeli M | Neuromuscular disorders : NMD | 2017 | PMID: 28688748 |
Improving genetic diagnosis in Mendelian disease with transcriptome sequencing. | Cummings BB | Science translational medicine | 2017 | PMID: 28424332 |
Mutations in POMGNT1 cause non-syndromic retinitis pigmentosa. | Xu M | Human molecular genetics | 2016 | PMID: 26908613 |
Novel POMGNT1 point mutations and intragenic rearrangements associated with muscle-eye-brain disease. | Saredi S | Journal of the neurological sciences | 2012 | PMID: 22554691 |
Cobblestone lissencephaly: neuropathological subtypes and correlations with genes of dystroglycanopathies. | Devisme L | Brain : a journal of neurology | 2012 | PMID: 22323514 |
Congenital muscular dystrophies with defective glycosylation of dystroglycan: a population study. | Mercuri E | Neurology | 2009 | PMID: 19299310 |
Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization. | Buratti E | Nucleic acids research | 2007 | PMID: 17576681 |
POMGnT1 mutation and phenotypic spectrum in muscle-eye-brain disease. | Diesen C | Journal of medical genetics | 2004 | PMID: 15466003 |
Statistical features of human exons and their flanking regions. | Zhang MQ | Human molecular genetics | 1998 | PMID: 9536098 |
Text-mined citations for rs386834024 ...
HelpRecord last updated Sep 08, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.