ClinVar Genomic variation as it relates to human health
NM_001750.7(CAST):c.1873del (p.Val625fs)
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_001750.7(CAST):c.1873del (p.Val625fs)
Variation ID: 189336 Accession: VCV000189336.3
- Type and length
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Deletion, 1 bp
- Location
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Cytogenetic: 5q15 5: 96762313 (GRCh38) [ NCBI UCSC ] 5: 96098017 (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 Aug 13, 2018 Aug 13, 2018 Mar 5, 2015 - HGVS
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Nucleotide Protein Molecular
consequenceNM_001750.7:c.1873del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001741.4:p.Val625fs frameshift NM_001042440.5:c.1750del NP_001035905.1:p.Val584fs frameshift NM_001042441.3:c.1816del NP_001035906.1:p.Val606fs frameshift NM_001042442.3:c.1807del NP_001035907.1:p.Val603fs frameshift NM_001042443.3:c.1624del NP_001035908.1:p.Val542fs frameshift NM_001042444.3:c.1501del NP_001035909.1:p.Val501fs frameshift NM_001042445.3:c.1519del NP_001035910.1:p.Val507fs frameshift NM_001042446.3:c.1462del NP_001035911.1:p.Val488fs frameshift NM_001190442.2:c.1585del NP_001177371.1:p.Val529fs frameshift NM_001284212.4:c.1501del NP_001271141.1:p.Val501fs frameshift NM_001284213.4:c.1408del NP_001271142.1:p.Val470fs frameshift NM_001329966.1:c.1807delG NP_001316895.1:p.Val603Trpfs frameshift NM_001330626.2:c.1777del NP_001317555.1:p.Val593fs frameshift NM_001330627.2:c.1750del NP_001317556.1:p.Val584fs frameshift NM_001330628.2:c.1705del NP_001317557.1:p.Val569fs frameshift NM_001330629.2:c.1789del NP_001317558.1:p.Val597fs frameshift NM_001330630.2:c.1462del NP_001317559.1:p.Val488fs frameshift NM_001330631.2:c.1585del NP_001317560.1:p.Val529fs frameshift NM_001330632.2:c.1558del NP_001317561.1:p.Val520fs frameshift NM_001330633.2:c.1567del NP_001317562.1:p.Val523fs frameshift NM_001330634.2:c.1528del NP_001317563.1:p.Val510fs frameshift NM_001349244.2:c.*887del 3 prime UTR NM_001375317.1:c.1762del NP_001362246.1:p.Val588fs frameshift NM_001423250.1:c.1624del NP_001410179.1:p.Val542fs frameshift NM_001423251.1:c.1585del NP_001410180.1:p.Val529fs frameshift NM_001423252.1:c.1585del NP_001410181.1:p.Val529fs frameshift NM_001423253.1:c.1558del NP_001410182.1:p.Val520fs frameshift NM_001423254.1:c.1558del NP_001410183.1:p.Val520fs frameshift NM_001423255.1:c.1519del NP_001410184.1:p.Val507fs frameshift NM_001423256.1:c.1519del NP_001410185.1:p.Val507fs frameshift NM_001423257.1:c.1519del NP_001410186.1:p.Val507fs frameshift NM_001423258.1:c.1519del NP_001410187.1:p.Val507fs frameshift NM_001423259.1:c.1519del NP_001410188.1:p.Val507fs frameshift NM_001423260.1:c.1462del NP_001410189.1:p.Val488fs frameshift NM_016442.5:c.*887del 3 prime UTR NM_173060.5:c.1558del NP_775083.1:p.Val520fs frameshift NR_104285.2:n.818del non-coding transcript variant NC_000005.10:g.96762313del NC_000005.9:g.96098017del NG_027839.2:g.178671del NG_029490.2:g.105277del - Protein change
- V507fs, V510fs, V523fs, V569fs, V470fs, V501fs, V542fs, V603fs, V625fs, V520fs, V597fs, V606fs, V488fs, V529fs, V584fs, V593fs, V588fs
- Other names
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- Canonical SPDI
- NC_000005.10:96762312: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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Allele frequency
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The frequency of the allele represented by this VCV record.
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Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
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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
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The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
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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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CAST | - | - |
GRCh38 GRCh37 |
140 | 513 | |
ERAP1 | - | - |
GRCh38 GRCh37 |
87 | 215 |
Conditions - Germline
Condition
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The condition for this variant-condition (RCV) record in ClinVar. |
Classification
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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
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The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
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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 (1) |
no assertion criteria provided
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Mar 5, 2015 | RCV000169752.13 |
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
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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
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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
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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
(Mar 05, 2015)
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no assertion criteria provided
Method: literature only
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PEELING SKIN WITH LEUKONYCHIA, ACRAL PUNCTATE KERATOSES, CHEILITIS, AND KNUCKLE PADS
Affected status: not provided
Allele origin:
germline
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OMIM
Accession: SCV000221302.2
First in ClinVar: Apr 11, 2015 Last updated: Aug 13, 2018 |
Comment on evidence:
In 2 brothers, 54 and 58 years of age (individuals 3 and 4, respectively), with peeling skin, leukonychia, acral punctate keratoses, cheilitis, and knuckle pads … (more)
In 2 brothers, 54 and 58 years of age (individuals 3 and 4, respectively), with peeling skin, leukonychia, acral punctate keratoses, cheilitis, and knuckle pads (PLACK; 616295), originally reported by Haber and Rose (1986), Lin et al. (2015) identified homozygosity for a 1-bp deletion, c.1750delG (c.1750delG, NM_001042440.3) in the CAST gene, causing a frameshift predicted to result in a premature termination codon (Val584TrpfsTer37). The mutation segregated with disease in the family. (less)
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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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Loss-of-function mutations in CAST cause peeling skin, leukonychia, acral punctate keratoses, cheilitis, and knuckle pads. | Lin Z | American journal of human genetics | 2015 | PMID: 25683118 |
Autosomal recessive pachyonychia congenita. | Haber RM | Archives of dermatology | 1986 | PMID: 3527073 |
Text-mined citations for rs786205141 ...
HelpRecord last updated Apr 20, 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.