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NM_001077365.2(POMT1):c.1598C>T (p.Ala533Val) AND Myopathy caused by variation in POMT1

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Aug 28, 2019
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:
RCV002470918.1

Allele description [Variation Report for NM_001077365.2(POMT1):c.1598C>T (p.Ala533Val)]

NM_001077365.2(POMT1):c.1598C>T (p.Ala533Val)

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.1598C>T (p.Ala533Val)
HGVS:
  • NC_000009.12:g.131520093C>T
  • NG_008896.1:g.22192C>T
  • NM_001077365.2:c.1598C>TMANE SELECT
  • NM_001077366.2:c.1436C>T
  • NM_001136113.2:c.1598C>T
  • NM_001136114.2:c.1247C>T
  • NM_001353193.2:c.1664C>T
  • NM_001353194.2:c.1436C>T
  • NM_001353195.2:c.1247C>T
  • NM_001353196.2:c.1508C>T
  • NM_001353197.2:c.1502C>T
  • NM_001353198.2:c.1502C>T
  • NM_001353199.2:c.1313C>T
  • NM_001353200.2:c.1142C>T
  • NM_001374689.1:c.1586C>T
  • NM_001374690.1:c.1379C>T
  • NM_001374691.1:c.1247C>T
  • NM_001374692.1:c.1247C>T
  • NM_001374693.1:c.1247C>T
  • NM_001374695.1:c.1208C>T
  • NM_007171.4:c.1664C>T
  • NP_001070833.1:p.Ala533Val
  • NP_001070834.1:p.Ala479Val
  • NP_001129585.1:p.Ala533Val
  • NP_001129586.1:p.Ala416Val
  • NP_001340122.2:p.Ala555Val
  • NP_001340123.1:p.Ala479Val
  • NP_001340124.1:p.Ala416Val
  • NP_001340125.1:p.Ala503Val
  • NP_001340126.2:p.Ala501Val
  • NP_001340127.2:p.Ala501Val
  • NP_001340128.2:p.Ala438Val
  • NP_001340129.1:p.Ala381Val
  • NP_001361618.1:p.Ala529Val
  • NP_001361619.1:p.Ala460Val
  • NP_001361620.1:p.Ala416Val
  • NP_001361621.1:p.Ala416Val
  • NP_001361622.1:p.Ala416Val
  • NP_001361624.1:p.Ala403Val
  • NP_009102.3:p.Ala555Val
  • NP_009102.4:p.Ala555Val
  • LRG_842t1:c.1664C>T
  • LRG_842t2:c.1598C>T
  • LRG_842p1:p.Ala555Val
  • LRG_842p2:p.Ala533Val
  • NC_000009.11:g.134395480C>T
  • NM_007171.3:c.1664C>T
  • NR_148391.2:n.1632C>T
  • NR_148392.2:n.1850C>T
  • NR_148393.2:n.1771C>T
  • NR_148394.2:n.1525C>T
  • NR_148395.2:n.1923C>T
  • NR_148396.2:n.1557C>T
  • NR_148397.2:n.1682C>T
  • NR_148398.2:n.1637C>T
  • NR_148399.2:n.2163C>T
  • NR_148400.2:n.1762C>T
Protein change:
A381V
Links:
dbSNP: rs199682341
NCBI 1000 Genomes Browser:
rs199682341
Molecular consequence:
  • NM_001077365.2:c.1598C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001077366.2:c.1436C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001136113.2:c.1598C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001136114.2:c.1247C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353193.2:c.1664C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353194.2:c.1436C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353195.2:c.1247C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353196.2:c.1508C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353197.2:c.1502C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353198.2:c.1502C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353199.2:c.1313C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353200.2:c.1142C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374689.1:c.1586C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374690.1:c.1379C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374691.1:c.1247C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374692.1:c.1247C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374693.1:c.1247C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374695.1:c.1208C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_007171.4:c.1664C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_148391.2:n.1632C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148392.2:n.1850C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148393.2:n.1771C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148394.2:n.1525C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148395.2:n.1923C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148396.2:n.1557C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148397.2:n.1682C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148398.2:n.1637C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148399.2:n.2163C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148400.2:n.1762C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
Myopathy caused by variation in POMT1
Identifiers:
MONDO: MONDO:0700070; MedGen: CN305641

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002767589Victorian Clinical Genetics Services, Murdoch Childrens Research Institute

See additional submitters

criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(Aug 28, 2019) 		germlineclinical testing

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

Help

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 Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, SCV002767589.1

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

Description

A heterozygous missense variant was identified, NM_007171.3(POMT1):c.1664C>T in exon 17 of 20 of the POMT1 gene. This substitution is predicted to create a minor amino acid change from alanine to valine at position 555 of the protein NP_009102.3(POMT1):p.(Ala555Val). The alanine at this position has low conservation (100 vertebrates, UCSC), and is located within the PMT_4TMC functional domain. In silico software predicts this variant to be benign (Polyphen, SIFT, CADD, Mutation Taster). The variant is present in the gnomAD population database at a frequency of 0.01% (37 heterozygotes, 0 homozygotes). The variant has been previously reported as a variant of uncertain significance (VUS) in ClinVar. Based on information available at the time of curation, this variant has been classified as a VARIANT of UNCERTAIN SIGNIFICANCE (VUS) with LOW CLINICAL RELEVANCE.

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

Last Updated: Jun 22, 2025