ClinVar Genomic variation as it relates to human health
NM_000390.4(CHM):c.1584_1587del (p.Val529fs)
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_000390.4(CHM):c.1584_1587del (p.Val529fs)
Variation ID: 11152 Accession: VCV000011152.13
- Type and length
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Microsatellite, 4 bp
- Location
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Cytogenetic: Xq21.2 X: 85878987-85878990 (GRCh38) [ NCBI UCSC ] X: 85133992-85133995 (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 Jun 15, 2017 Jul 23, 2024 Jan 4, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000390.4:c.1580_1583delTGTT MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
frameshift NM_000390.4:c.1584_1587del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000381.1:p.Val529fs frameshift NM_000390.2:c.1584_1587delTGTT NM_001320959.1:c.1140_1143del NP_001307888.1:p.Val381fs frameshift NM_001362517.1:c.1140_1143del NP_001349446.1:p.Val381fs frameshift NM_001362518.2:c.1140_1143del NP_001349447.1:p.Val381fs frameshift NM_001362519.1:c.1140_1143del NP_001349448.1:p.Val381fs frameshift NC_000023.11:g.85878988ACAA[1] NC_000023.10:g.85133993ACAA[1] NG_009874.2:g.173569TGTT[1] LRG_699:g.173569TGTT[1] LRG_699t1:c.1584_1587del - Protein change
- V529fs, V381fs
- Other names
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- Canonical SPDI
- NC_000023.11:85878986:AACAAACAA:AACAA
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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
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The frequency of the allele represented by this VCV record.
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- Links
- Comment on variant
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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CHM | Sufficient evidence for dosage pathogenicity | No evidence available |
GRCh38 GRCh37 |
798 | 1027 |
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 (3) |
criteria provided, single submitter
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Feb 2, 2022 | RCV000011902.13 | |
Pathogenic (1) |
criteria provided, single submitter
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Apr 25, 2019 | RCV001073513.2 | |
Pathogenic (2) |
criteria provided, multiple submitters, no conflicts
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Jan 4, 2024 | RCV001386024.6 |
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
(Feb 02, 2022)
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criteria provided, single submitter
Method: clinical testing
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Choroideremia
(X-linked dominant inheritance)
Affected status: unknown
Allele origin:
germline
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Victorian Clinical Genetics Services, Murdoch Childrens Research Institute
Additional submitter:
Shariant Australia, Australian Genomics
Accession: SCV002557975.2
First in ClinVar: Aug 08, 2022 Last updated: Jul 23, 2024 |
Comment:
Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as a Pathogenic. Following criteria are met: 0102 - Loss of function is a known … (more)
Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as a Pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with Choroideremia (MIM# 303100). (I) 0110 - This gene is associated with X-linked disease. Males are predominantly affected, while females are usually unaffected some may display symptoms similar to affected males due to random X-inactivation (PMID: 29555028). (I) 0201 - Variant is predicted to cause nonsense-mediated decay (NMD) and loss of protein (premature termination codon is located at least 54 nucleotides upstream of the final exon-exon junction). (SP) 0251 - This variant is heterozygous. (I) 0302 - Variant is present in gnomAD (v3) <0.001 for a dominant condition (1 heterozygote, 0 homozygotes, hemizygotes). (SP) 0701 - Other NMD-predicted variants comparable to the one identified in this case have very strong previous evidence for pathogenicity (ClinVar). (SP) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant has been reported in multiple individuals with choroideremia (ClinVar, PMID: 27739455, 33110609). (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
(Apr 25, 2019)
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criteria provided, single submitter
Method: clinical testing
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Retinal dystrophy
Affected status: yes
Allele origin:
germline
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Blueprint Genetics
Accession: SCV001239059.1
First in ClinVar: Apr 18, 2020 Last updated: Apr 18, 2020
Comment:
My Retina Tracker patient
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Pathogenic
(May 26, 2023)
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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: SCV003930935.1
First in ClinVar: Jun 17, 2023 Last updated: Jun 17, 2023 |
Comment:
Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Not … (more)
Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 31922496, 18087237, 1598901, 25912515, 28752371, 30541579, 27739455, 31097864, 35040292, 33573424, 27936069, 24913019, 12203991, 33110609, 8242078) (less)
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Pathogenic
(Jan 04, 2024)
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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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Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV001586109.4
First in ClinVar: May 10, 2021 Last updated: Feb 14, 2024 |
Comment:
This sequence change creates a premature translational stop signal (p.Val529Hisfs*7) in the CHM gene. It is expected to result in an absent or disrupted protein … (more)
This sequence change creates a premature translational stop signal (p.Val529Hisfs*7) in the CHM gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in CHM are known to be pathogenic (PMID: 9067750, 23811034). This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individual(s) with clinical features of choroideremia (PMID: 25912515, 30541579, 31181178). ClinVar contains an entry for this variant (Variation ID: 11152). For these reasons, this variant has been classified as Pathogenic. (less)
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Pathogenic
(Aug 01, 2014)
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no assertion criteria provided
Method: literature only
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CHOROIDEREMIA
Affected status: not provided
Allele origin:
germline
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OMIM
Accession: SCV000032135.3
First in ClinVar: Apr 04, 2013 Last updated: Jun 15, 2017 |
Comment on evidence:
Using PCR-SSCP analysis and direct DNA sequencing, van den Hurk et al. (1992) detected and characterized different mutations in the CHM gene in 5 patients … (more)
Using PCR-SSCP analysis and direct DNA sequencing, van den Hurk et al. (1992) detected and characterized different mutations in the CHM gene in 5 patients with choroideremia (CHM; 303100). Patient 2086 had a 4-bp deletion (delTGTT) in exon 'C,' causing a frameshift predicted to result in premature termination at codon 198. Van den Hurk et al. (1997) referred to this mutation as 1614_1617delTGTT in exon 13. In a Danish patient with choroideremia, Schwartz et al. (1993) identified the same 4-bp deletion in exon 'C' of the CHM gene. Noting that this deletion was identical to that found by van den Hurk et al. (1992) in a German family with choroideremia, Schwartz et al. (1993) suggested that it may represent a mutational hotspot that is susceptible to slippage during replication since the TGTT sequence is duplicated in the normal sequence position. In a 3-generation French family with choroideremia, consisting of 3 affected males, 5 carrier females, and 1 unaffected male, Pascal et al. (1993) analyzed 5 exons of the CHM gene and identified the same 4-bp deletion. In a 21-year-old Chinese man with retinal degeneration that was initially diagnosed as retinitis pigmentosa (see 268000), Li et al. (2014) identified the recurrent 4-bp deletion, which they designated c.1584_1587delTGTT, in exon 13 of the CHM gene. Review of fundus images showed changes consistent with choroideremia. The patient had an affected maternal uncle. Examination of the proband's obligate carrier mother, who had normal visual acuity without night blindness, revealed a number of yellow crystalline-like spots in the macular area and irregular mottled pigmentation in the midperiphery. Electroretinography showed normal rod responses and mildly reduced cone responses. (less)
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not provided
(-)
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no classification provided
Method: literature only
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Choroideremia
Affected status: unknown
Allele origin:
germline
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GeneReviews
Accession: SCV002029118.2
First in ClinVar: Dec 04, 2021 Last updated: Oct 01, 2022 |
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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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Expanding the genetic spectrum of choroideremia in an Australian cohort: report of five novel CHM variants. | McLaren TL | Human genome variation | 2020 | PMID: 33110609 |
Spectrum of Disease Severity and Phenotype in Choroideremia Carriers. | Jauregui R | American journal of ophthalmology | 2019 | PMID: 31181178 |
Novel CHM mutations in Polish patients with choroideremia - an orphan disease with close perspective of treatment. | Skorczyk-Werner A | Orphanet journal of rare diseases | 2018 | PMID: 30541579 |
Molecular genetics characterization and homology modeling of the CHM gene mutation: A study on its association with choroideremia. | Imani S | Mutation research. Reviews in mutation research | 2018 | PMID: 29555028 |
Novel CHM mutations identified in Chinese families with Choroideremia. | Cai XB | Scientific reports | 2016 | PMID: 27739455 |
Genetic analysis of choroideremia families in the Australian population. | McLaren TL | Clinical & experimental ophthalmology | 2015 | PMID: 25912515 |
Exome sequencing reveals CHM mutations in six families with atypical choroideremia initially diagnosed as retinitis pigmentosa. | Li S | International journal of molecular medicine | 2014 | PMID: 24913019 |
A clinical molecular genetic service for United Kingdom families with choroideraemia. | Ramsden SC | European journal of medical genetics | 2013 | PMID: 23811034 |
Mouse choroideremia gene mutation causes photoreceptor cell degeneration and is not transmitted through the female germline. | van den Hurk JA | Human molecular genetics | 1997 | PMID: 9175730 |
Molecular basis of choroideremia (CHM): mutations involving the Rab escort protein-1 (REP-1) gene. | van den Hurk JA | Human mutation | 1997 | PMID: 9067750 |
Identification of mutations in Danish choroideremia families. | Schwartz M | Human mutation | 1993 | PMID: 8477262 |
A new (old) deletion in the choroideremia gene. | Pascal O | Human molecular genetics | 1993 | PMID: 8242078 |
Detection and characterization of point mutations in the choroideremia candidate gene by PCR-SSCP analysis and direct DNA sequencing. | van den Hurk JA | American journal of human genetics | 1992 | PMID: 1598901 |
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Text-mined citations for rs587776746 ...
HelpRecord last updated Sep 29, 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.
NCBI staff reviewed the sequence information reported in PubMed 8477262 Table 1 to determine the location of this allele on the current reference sequence.