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NM_001077365.2(POMT1):c.1125C>T (p.His375=)

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
6 (Most recent: Jan 7, 2021)
Last evaluated:
Dec 3, 2020
Accession:
VCV000130005.6
Variation ID:
130005
Description:
single nucleotide variant
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NM_001077365.2(POMT1):c.1125C>T (p.His375=)

Allele ID
135451
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
9q34.13
Genomic location
9: 131513281 (GRCh38) GRCh38 UCSC
9: 134388668 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_842t2:c.1125C>T LRG_842p2:p.His375=
LRG_842t1:c.1191C>T LRG_842p1:p.His397=
NC_000009.11:g.134388668C>T
... more HGVS
Protein change
-
Other names
p.H397H:CAC>CAT
Canonical SPDI
NC_000009.12:131513280:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.01218 (T)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.01031
The Genome Aggregation Database (gnomAD) 0.00919
The Genome Aggregation Database (gnomAD) 0.01019
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.01099
1000 Genomes Project 0.01218
Links
ClinGen: CA154743
dbSNP: rs35242383
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 3 criteria provided, multiple submitters, no conflicts Jul 29, 2014 RCV000118029.6
Likely benign 1 criteria provided, single submitter Jan 12, 2018 RCV000281358.2
Benign 1 criteria provided, single submitter May 30, 2017 RCV000576492.3
Benign 1 criteria provided, single submitter Dec 3, 2020 RCV001081388.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
POMT1 - - GRCh38
GRCh37
570 608

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Jul 29, 2014)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000196865.10
Submitted: (Mar 26, 2018)
Evidence details
Comment:
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at … (more)
Benign
(-)
criteria provided, single submitter
Method: clinical testing
NOT SPECIFIED
Allele origin: germline
PreventionGenetics,PreventionGenetics
Accession: SCV000311728.1
Submitted: (Apr 28, 2016)
Evidence details
Benign
(May 30, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV000677413.2
Submitted: (Aug 31, 2018)
Evidence details
Likely benign
(Jan 12, 2018)
criteria provided, single submitter
Method: clinical testing
Limb-girdle muscular dystrophy-dystroglycanopathy, type C1
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000477659.3
Submitted: (Feb 20, 2020)
Evidence details
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)
Benign
(Dec 03, 2020)
criteria provided, single submitter
Method: clinical testing
Congenital muscular dystrophy-dystroglycanopathy with mental retardation, type B1
Walker-Warburg congenital muscular dystrophy
Limb-girdle muscular dystrophy-dystroglycanopathy, type C1
Allele origin: germline
Invitae
Accession: SCV000649868.5
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
AllHighlyPenetrant
(Autosomal recessive inheritance)
Allele origin: germline
Genetic Services Laboratory,University of Chicago
Accession: SCV000152349.2
Submitted: (Jun 27, 2014)
Evidence details
Comment:
Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated … (more)

Functional evidence

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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 this variant

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There are no citations in ClinVar for this variation. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs35242383...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Dec 04, 2021