ClinVar Genomic variation as it relates to human health
NM_001077365.2(POMT1):c.1856C>T (p.Ala619Val)
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_001077365.2(POMT1):c.1856C>T (p.Ala619Val)
Variation ID: 130011 Accession: VCV000130011.19
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 9q34.13 9: 134397464 (GRCh37) [ NCBI UCSC ] 9: 131522077 (GRCh38) [ 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 May 17, 2014 Feb 28, 2024 Jan 31, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_001077365.2:c.1856C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001070833.1:p.Ala619Val missense NM_001077366.2:c.1694C>T NP_001070834.1:p.Ala565Val missense NM_001136113.2:c.1856C>T NP_001129585.1:p.Ala619Val missense NM_001136114.2:c.1505C>T NP_001129586.1:p.Ala502Val missense NM_001353193.2:c.1922C>T NP_001340122.2:p.Ala641Val missense NM_001353194.2:c.1694C>T NP_001340123.1:p.Ala565Val missense NM_001353195.2:c.1505C>T NP_001340124.1:p.Ala502Val missense NM_001353196.2:c.1766C>T NP_001340125.1:p.Ala589Val missense NM_001353197.2:c.1760C>T NP_001340126.2:p.Ala587Val missense NM_001353198.2:c.1760C>T NP_001340127.2:p.Ala587Val missense NM_001353199.2:c.1571C>T NP_001340128.2:p.Ala524Val missense NM_001353200.2:c.1400C>T NP_001340129.1:p.Ala467Val missense NM_001374689.1:c.1844C>T NP_001361618.1:p.Ala615Val missense NM_001374690.1:c.1637C>T NP_001361619.1:p.Ala546Val missense NM_001374691.1:c.1505C>T NP_001361620.1:p.Ala502Val missense NM_001374692.1:c.1505C>T NP_001361621.1:p.Ala502Val missense NM_001374693.1:c.1505C>T NP_001361622.1:p.Ala502Val missense NM_001374695.1:c.1466C>T NP_001361624.1:p.Ala489Val missense NM_007171.4:c.1922C>T NP_009102.4:p.Ala641Val missense NR_148391.2:n.1890C>T non-coding transcript variant NR_148392.2:n.2108C>T non-coding transcript variant NR_148393.2:n.2029C>T non-coding transcript variant NR_148394.2:n.1783C>T non-coding transcript variant NR_148395.2:n.2181C>T non-coding transcript variant NR_148396.2:n.1815C>T non-coding transcript variant NR_148397.2:n.1940C>T non-coding transcript variant NR_148398.2:n.1895C>T non-coding transcript variant NR_148399.2:n.2421C>T non-coding transcript variant NR_148400.2:n.2020C>T non-coding transcript variant NC_000009.12:g.131522077C>T NC_000009.11:g.134397464C>T NG_008896.1:g.24176C>T LRG_842t1:c.1922C>T LRG_842p1:p.Ala641Val LRG_842t2:c.1856C>T LRG_842p2:p.Ala619Val - Protein change
- A641V, A502V, A524V, A565V, A587V, A589V, A467V, A619V, A615V, A489V, A546V
- Other names
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- Canonical SPDI
- NC_000009.12:131522076:C:T
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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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0.02097 (T)
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Allele frequency
Help
The frequency of the allele represented by this VCV record.
The Genome Aggregation Database (gnomAD), exomes 0.00665
Exome Aggregation Consortium (ExAC) 0.00758
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.01569
The Genome Aggregation Database (gnomAD) 0.01621
Trans-Omics for Precision Medicine (TOPMed) 0.01684
1000 Genomes Project 0.02097
1000 Genomes Project 30x 0.02217
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
Help
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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POMT1 | - | - |
GRCh38 GRCh37 |
1135 | 1176 |
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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Benign (2) |
criteria provided, multiple submitters, no conflicts
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Aug 15, 2013 | RCV000118035.11 | |
Likely benign (1) |
criteria provided, single submitter
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Apr 27, 2017 | RCV000331368.6 | |
Benign (2) |
criteria provided, multiple submitters, no conflicts
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Nov 1, 2017 | RCV000712821.6 | |
Benign (1) |
criteria provided, single submitter
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Jan 31, 2024 | RCV001085455.8 |
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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Benign
(Nov 01, 2017)
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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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Athena Diagnostics Inc
Accession: SCV000843355.1
First in ClinVar: Oct 20, 2018 Last updated: Oct 20, 2018 |
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Likely benign
(Apr 27, 2017)
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criteria provided, single submitter
Method: clinical testing
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Autosomal recessive limb-girdle muscular dystrophy type 2K
Affected status: unknown
Allele origin:
germline
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Illumina Laboratory Services, Illumina
Accession: SCV000477674.3
First in ClinVar: Dec 06, 2016 Last updated: May 31, 2020 |
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. (less)
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Benign
(Jan 31, 2024)
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criteria provided, single submitter
Method: clinical testing
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Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B1
Walker-Warburg congenital muscular dystrophy Autosomal recessive limb-girdle muscular dystrophy type 2K
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: SCV000649888.8
First in ClinVar: Dec 26, 2017 Last updated: Feb 28, 2024 |
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Benign
(Aug 15, 2013)
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criteria provided, single submitter
Method: clinical testing
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AllHighlyPenetrant
(Autosomal recessive inheritance)
Affected status: unknown
Allele origin:
germline
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Genetic Services Laboratory, University of Chicago
Accession: SCV000152356.1
First in ClinVar: May 17, 2014 Last updated: May 17, 2014 |
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Benign
(-)
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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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PreventionGenetics, part of Exact Sciences
Accession: SCV000311748.1
First in ClinVar: Oct 02, 2016 Last updated: Oct 02, 2016 |
|
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Benign
(Mar 03, 2015)
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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: SCV001945140.2
First in ClinVar: Sep 29, 2021 Last updated: Mar 04, 2023 |
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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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Genetic alterations of protein-o-mannosyltransferase-1 in glioneuronal and glial brain tumors with subarachnoid spread. | Snoei J | Neuropathology : official journal of the Japanese Society of Neuropathology | 2009 | PMID: 18647264 |
Refining genotype phenotype correlations in muscular dystrophies with defective glycosylation of dystroglycan. | Godfrey C | Brain : a journal of neurology | 2007 | PMID: 17878207 |
The expanding phenotype of POMT1 mutations: from Walker-Warburg syndrome to congenital muscular dystrophy, microcephaly, and mental retardation. | van Reeuwijk J | Human mutation | 2006 | PMID: 16575835 |
Text-mined citations for rs12115566 ...
HelpRecord last updated Mar 11, 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.