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NM_001077365.2(POMT1):c.132A>C (p.Glu44Asp) AND POMT1-related disorder

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Apr 17, 2023
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV004529856.1

Allele description [Variation Report for NM_001077365.2(POMT1):c.132A>C (p.Glu44Asp)]

NM_001077365.2(POMT1):c.132A>C (p.Glu44Asp)

Gene:
POMT1:protein O-mannosyltransferase 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
9q34.13
Genomic location:
Preferred name:
NM_001077365.2(POMT1):c.132A>C (p.Glu44Asp)
HGVS:
  • NC_000009.12:g.131506123A>C
  • NG_008896.1:g.8222A>C
  • NM_001077365.2:c.132A>CMANE SELECT
  • NM_001077366.2:c.-31A>C
  • NM_001136113.2:c.132A>C
  • NM_001136114.2:c.-122-280A>C
  • NM_001353193.2:c.132A>C
  • NM_001353194.2:c.-31A>C
  • NM_001353195.2:c.-122-280A>C
  • NM_001353196.2:c.123-280A>C
  • NM_001353197.2:c.-31A>C
  • NM_001353198.2:c.-31A>C
  • NM_001353199.2:c.-122-280A>C
  • NM_001353200.2:c.-80-280A>C
  • NM_001374689.1:c.-31A>C
  • NM_001374690.1:c.132A>C
  • NM_001374691.1:c.-71-1245A>C
  • NM_001374692.1:c.-71-1245A>C
  • NM_001374693.1:c.-31A>C
  • NM_001374695.1:c.-30+1783A>C
  • NM_007171.4:c.132A>C
  • NP_001070833.1:p.Glu44Asp
  • NP_001129585.1:p.Glu44Asp
  • NP_001340122.2:p.Glu44Asp
  • NP_001361619.1:p.Glu44Asp
  • NP_009102.3:p.Glu44Asp
  • NP_009102.3:p.Glu44Asp
  • NP_009102.4:p.Glu44Asp
  • LRG_842t1:c.132A>C
  • LRG_842t2:c.132A>C
  • LRG_842p1:p.Glu44Asp
  • LRG_842p2:p.Glu44Asp
  • NC_000009.11:g.134381510A>C
  • NM_007171.3:c.132A>C
  • NR_148391.2:n.166A>C
  • NR_148392.2:n.318A>C
  • NR_148393.2:n.166A>C
  • NR_148394.2:n.166A>C
  • NR_148395.2:n.318A>C
  • NR_148398.2:n.166A>C
  • NR_148399.2:n.558A>C
Protein change:
E44D
Links:
dbSNP: rs398124244
NCBI 1000 Genomes Browser:
rs398124244
Molecular consequence:
  • NM_001077366.2:c.-31A>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001353194.2:c.-31A>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001353197.2:c.-31A>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001353198.2:c.-31A>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001374689.1:c.-31A>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001374693.1:c.-31A>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001136114.2:c.-122-280A>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001353195.2:c.-122-280A>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001353196.2:c.123-280A>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001353199.2:c.-122-280A>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001353200.2:c.-80-280A>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001374691.1:c.-71-1245A>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001374692.1:c.-71-1245A>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001374695.1:c.-30+1783A>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001077365.2:c.132A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001136113.2:c.132A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353193.2:c.132A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374690.1:c.132A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_007171.4:c.132A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NR_148391.2:n.166A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148392.2:n.318A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148393.2:n.166A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148394.2:n.166A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148395.2:n.318A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148398.2:n.166A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148399.2:n.558A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
POMT1-related disorder
Synonyms:
POMT1-Related Disorders; POMT1-related condition
Identifiers:

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV004113553PreventionGenetics, part of Exact Sciences
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenic
(Apr 17, 2023)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From PreventionGenetics, part of Exact Sciences, SCV004113553.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

The POMT1 c.132A>C variant is predicted to result in the amino acid substitution p.Glu44Asp. This variant was reported in the compound heterozygous state in an individual with congenital muscular dystrophy (Table e-1 and e-3, Patient ID 102, O'Grady et al. 2016. PubMed ID: 27159402). Of note, another variant impacting the same amino acid was also reported in the compound heterozygous state in an individual with mild congenital muscular dystrophy [c.130G>A (pl.Glu44Lys), Case 3, Yang et al. 2016. PubMed ID: 27193224). This variant is reported in 0.0039% of alleles in individuals of European (Non-Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/9-134381510-A-C). This variant is interpreted as likely pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Jul 23, 2024