NM_001077365.2(POMT1):c.1390T>G (p.Trp464Gly) AND multiple conditions

Clinical significance:Uncertain significance (Last evaluated: Feb 17, 2020)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001295034.1

Allele description [Variation Report for NM_001077365.2(POMT1):c.1390T>G (p.Trp464Gly)]

NM_001077365.2(POMT1):c.1390T>G (p.Trp464Gly)

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.1390T>G (p.Trp464Gly)
HGVS:
  • NC_000009.12:g.131518861T>G
  • NG_008896.1:g.20960T>G
  • NM_001077365.2:c.1390T>GMANE SELECT
  • NM_001077366.2:c.1228T>G
  • NM_001136113.2:c.1390T>G
  • NM_001136114.2:c.1039T>G
  • NM_001353193.2:c.1456T>G
  • NM_001353194.2:c.1228T>G
  • NM_001353195.2:c.1039T>G
  • NM_001353196.2:c.1300T>G
  • NM_001353197.2:c.1294T>G
  • NM_001353198.2:c.1294T>G
  • NM_001353199.2:c.1105T>G
  • NM_001353200.2:c.934T>G
  • NM_001374689.1:c.1378T>G
  • NM_001374690.1:c.1365+324T>G
  • NM_001374691.1:c.1039T>G
  • NM_001374692.1:c.1039T>G
  • NM_001374693.1:c.1039T>G
  • NM_001374695.1:c.1000T>G
  • NM_007171.4:c.1456T>G
  • NP_001070833.1:p.Trp464Gly
  • NP_001070834.1:p.Trp410Gly
  • NP_001129585.1:p.Trp464Gly
  • NP_001129586.1:p.Trp347Gly
  • NP_001340122.2:p.Trp486Gly
  • NP_001340123.1:p.Trp410Gly
  • NP_001340124.1:p.Trp347Gly
  • NP_001340125.1:p.Trp434Gly
  • NP_001340126.2:p.Trp432Gly
  • NP_001340127.2:p.Trp432Gly
  • NP_001340128.2:p.Trp369Gly
  • NP_001340129.1:p.Trp312Gly
  • NP_001361618.1:p.Trp460Gly
  • NP_001361620.1:p.Trp347Gly
  • NP_001361621.1:p.Trp347Gly
  • NP_001361622.1:p.Trp347Gly
  • NP_001361624.1:p.Trp334Gly
  • NP_009102.4:p.Trp486Gly
  • LRG_842t1:c.1456T>G
  • LRG_842t2:c.1390T>G
  • LRG_842p1:p.Trp486Gly
  • LRG_842p2:p.Trp464Gly
  • NC_000009.11:g.134394248T>G
  • NR_148391.2:n.1424T>G
  • NR_148392.2:n.1642T>G
  • NR_148393.2:n.1563T>G
  • NR_148394.2:n.1317T>G
  • NR_148395.2:n.1715T>G
  • NR_148396.2:n.1349T>G
  • NR_148397.2:n.1474T>G
  • NR_148398.2:n.1429T>G
  • NR_148399.2:n.1955T>G
  • NR_148400.2:n.1554T>G
Protein change:
W312G
Molecular consequence:
  • NM_001374690.1:c.1365+324T>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001077365.2:c.1390T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001077366.2:c.1228T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001136113.2:c.1390T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001136114.2:c.1039T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353193.2:c.1456T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353194.2:c.1228T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353195.2:c.1039T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353196.2:c.1300T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353197.2:c.1294T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353198.2:c.1294T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353199.2:c.1105T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353200.2:c.934T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374689.1:c.1378T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374691.1:c.1039T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374692.1:c.1039T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374693.1:c.1039T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374695.1:c.1000T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_007171.4:c.1456T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NR_148391.2:n.1424T>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148392.2:n.1642T>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148393.2:n.1563T>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148394.2:n.1317T>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148395.2:n.1715T>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148396.2:n.1349T>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148397.2:n.1474T>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148398.2:n.1429T>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148399.2:n.1955T>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148400.2:n.1554T>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
Limb-girdle muscular dystrophy-dystroglycanopathy, type C1 (MDDGC1)
Synonyms:
MUSCULAR DYSTROPHY-DYSTROGLYCANOPATHY (LIMB-GIRDLE), TYPE C, 1; MUSCULAR DYSTROPHY, LIMB-GIRDLE, TYPE 2K; MUSCULAR DYSTROPHY, LIMB-GIRDLE, AUTOSOMAL RECESSIVE 11
Identifiers:
MONDO: MONDO:0012248; MedGen: C1836373; Orphanet: 86812; OMIM: 609308
Name:
Congenital muscular dystrophy-dystroglycanopathy with mental retardation, type B1 (MDDGB1)
Synonyms:
MUSCULAR DYSTROPHY, CONGENITAL, POMT1-RELATED; MUSCULAR DYSTROPHY-DYSTROGLYCANOPATHY (CONGENITAL WITH IMPAIRED INTELLECTUAL IMPAIRMENT), TYPE B, 1; Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B1
Identifiers:
MONDO: MONDO:0013159; MedGen: C3150415; OMIM: 613155
Name:
Walker-Warburg congenital muscular dystrophy (MDDGA1)
Synonyms:
HARD syndrome; Muscular dystrophy-dystroglycanopathy, type A; Walker-Warburg syndrome
Identifiers:
MONDO: MONDO:0000171; MedGen: C0265221; Orphanet: 899; OMIM: PS236670

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001483943Invitaecriteria provided, single submitter
Uncertain significance
(Feb 17, 2020)
germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Summary from all submissions

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

Citations

PubMed

Analysis of phenotype, enzyme activity and genotype of Chinese patients with POMT1 mutation.

Yang H, Manya H, Kobayashi K, Jiao H, Fu X, Xiao J, Li X, Wang J, Jiang Y, Toda T, Endo T, Wu X, Xiong H.

J Hum Genet. 2016 Aug;61(8):753-9. doi: 10.1038/jhg.2016.42. Epub 2016 May 19.

PubMed [citation]
PMID:
27193224

Compound heterozygous POMT1 mutations in a Chinese family with autosomal recessive muscular dystrophy-dystroglycanopathy C1.

Hu P, Wu S, Yuan L, Lin Q, Zheng W, Xia H, Xu H, Guan L, Deng H.

J Cell Mol Med. 2017 Jul;21(7):1388-1393. doi: 10.1111/jcmm.13068. Epub 2017 Feb 3.

PubMed [citation]
PMID:
28157257
PMCID:
PMC5487925
See all PubMed Citations (3)

Details of each submission

From Invitae, SCV001483943.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

This sequence change replaces tryptophan with glycine at codon 486 of the POMT1 protein (p.Trp486Gly). The tryptophan residue is highly conserved and there is a large physicochemical difference between tryptophan and glycine. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with POMT1-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. This variant disrupts the p.p.Trp486 amino acid residue in POMT1. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 27193224, 28157257). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

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

Last Updated: Jun 14, 2021

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