ClinVar Genomic variation as it relates to human health
NM_017837.4(PIGV):c.349A>G (p.Ile117Val)
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.
Uncertain significance(5); Likely benign(2)
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_017837.4(PIGV):c.349A>G (p.Ile117Val)
Variation ID: 297116 Accession: VCV000297116.17
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 1p36.11 1: 26794383 (GRCh38) [ NCBI UCSC ] 1: 27120874 (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 Dec 6, 2016 Mar 16, 2024 Oct 28, 2022 - HGVS
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Nucleotide Protein Molecular
consequenceNM_017837.4:c.349A>G MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_060307.2:p.Ile117Val missense NM_001202554.2:c.349A>G NP_001189483.1:p.Ile117Val missense NM_001374478.1:c.349A>G NP_001361407.1:p.Ile117Val missense NM_001374480.1:c.349A>G NP_001361409.1:p.Ile117Val missense NM_001374481.1:c.349A>G NP_001361410.1:p.Ile117Val missense NM_001374482.1:c.349A>G NP_001361411.1:p.Ile117Val missense NM_001374483.1:c.-33A>G 5 prime UTR NM_001374484.1:c.172+177A>G intron variant NM_001374485.1:c.172+177A>G intron variant NM_001374486.1:c.79-3180A>G intron variant NR_164651.1:n.847A>G non-coding transcript variant NC_000001.11:g.26794383A>G NC_000001.10:g.27120874A>G NG_028133.1:g.11421A>G - Protein change
- I117V
- Other names
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- Canonical SPDI
- NC_000001.11:26794382:A:G
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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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0.00080 (G)
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Allele frequency
Help
The frequency of the allele represented by this VCV record.
1000 Genomes Project 0.00080
1000 Genomes Project 30x 0.00094
The Genome Aggregation Database (gnomAD) 0.00097
Trans-Omics for Precision Medicine (TOPMed) 0.00104
The Genome Aggregation Database (gnomAD), exomes 0.00139
Exome Aggregation Consortium (ExAC) 0.00158
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
Help
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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PIGV | - | - |
GRCh38 GRCh37 |
326 | 335 |
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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Uncertain significance (2) |
criteria provided, multiple submitters, no conflicts
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Jun 18, 2020 | RCV000286962.6 | |
Uncertain significance (1) |
criteria provided, single submitter
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Mar 29, 2016 | RCV000455981.4 | |
Conflicting interpretations of pathogenicity (3) |
criteria provided, conflicting classifications
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Oct 28, 2022 | RCV000514626.9 | |
Likely benign (1) |
criteria provided, single submitter
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Jun 22, 2022 | RCV003920207.1 |
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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Uncertain significance
(Mar 29, 2016)
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criteria provided, single submitter
Method: clinical testing
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not specified
Affected status: unknown
Allele origin:
germline
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Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
Accession: SCV000540033.1
First in ClinVar: Apr 09, 2017 Last updated: Apr 09, 2017 |
Comment:
Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or … (more)
Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: See c.348G>A. These two variants result in c.348_349delinsAG. (p.Ile117Val). Not reported. MAF 0.25%. Gene is associated with AR hyperphosphatasia with mental retardation syndrome. Severe end of the spectrum presents with multiple congenital anomalies, including Hirschsprung disease, vesicoureteral, and renal anomalies as well as anorectal malformations. Developmental delays, particular facial anomalies, brachytelephalangy, and hyperphosphatasia are consistently found. VUS3, but the gene may explain the patient's phenotype, so may report in IBA report. - OB 10/22/15: Decided to not include in the report, since it is a VUS3 in a recessive gene not well-associated with the patient's pehnotype, and the variant is heterozygous. (less)
Method: Genome/Exome Filtration
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Uncertain significance
(May 19, 2017)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: not provided
Allele origin:
germline
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Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics
Accession: SCV000609667.1
First in ClinVar: Nov 05, 2017 Last updated: Nov 05, 2017 |
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Likely benign
(Dec 31, 2019)
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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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Invitae
Accession: SCV001110038.2
First in ClinVar: Dec 17, 2019 Last updated: May 04, 2020 |
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Uncertain significance
(Jan 12, 2018)
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criteria provided, single submitter
Method: clinical testing
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Hyperphosphatasia with intellectual disability syndrome 1
Affected status: unknown
Allele origin:
germline
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Illumina Laboratory Services, Illumina
Accession: SCV000357200.3
First in ClinVar: Dec 06, 2016 Last updated: May 31, 2020 |
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. (less)
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Uncertain significance
(Jun 18, 2020)
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criteria provided, single submitter
Method: clinical testing
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Hyperphosphatasia with intellectual disability syndrome 1
Affected status: unknown
Allele origin:
germline
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New York Genome Center
Study: CSER-NYCKidSeq
Accession: SCV002098008.1 First in ClinVar: Feb 20, 2022 Last updated: Feb 20, 2022 |
Clinical Features:
Seizure (present) , Cluster headache (present) , Attention deficit hyperactivity disorder (present) , Decreased circulating antibody level (present) , Anxiety (present) , Gastroesophageal reflux (present)
Secondary finding: no
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Uncertain significance
(Oct 28, 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: SCV003921609.1
First in ClinVar: May 06, 2023 Last updated: May 06, 2023 |
Comment:
In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
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Likely benign
(Jun 22, 2022)
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criteria provided, single submitter
Method: clinical testing
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PIGV-related condition
Affected status: unknown
Allele origin:
germline
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PreventionGenetics, part of Exact Sciences
Accession: SCV004729175.1
First in ClinVar: Mar 16, 2024 Last updated: Mar 16, 2024 |
Comment:
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).
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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
HelpThere are no citations for germline classification of this variant in ClinVar. If you know of citations for this variation, please consider submitting that information to ClinVar. |
Text-mined citations for rs142192097 ...
HelpRecord last updated Mar 17, 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.