NM_001077365.2(POMT1):c.1252G>A (p.Ala418Thr) AND multiple conditions

Clinical significance:Uncertain significance (Last evaluated: Mar 18, 2020)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001243330.2

Allele description [Variation Report for NM_001077365.2(POMT1):c.1252G>A (p.Ala418Thr)]

NM_001077365.2(POMT1):c.1252G>A (p.Ala418Thr)

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.1252G>A (p.Ala418Thr)
HGVS:
  • NC_000009.12:g.131515502G>A
  • NG_008896.1:g.17601G>A
  • NM_001077365.2:c.1252G>AMANE SELECT
  • NM_001077366.2:c.1090G>A
  • NM_001136113.2:c.1252G>A
  • NM_001136114.2:c.901G>A
  • NM_001353193.2:c.1318G>A
  • NM_001353194.2:c.1090G>A
  • NM_001353195.2:c.901G>A
  • NM_001353196.2:c.1162G>A
  • NM_001353197.2:c.1156G>A
  • NM_001353198.2:c.1156G>A
  • NM_001353199.2:c.967G>A
  • NM_001353200.2:c.796G>A
  • NM_001374689.1:c.1240G>A
  • NM_001374690.1:c.1252G>A
  • NM_001374691.1:c.901G>A
  • NM_001374692.1:c.901G>A
  • NM_001374693.1:c.901G>A
  • NM_001374695.1:c.862G>A
  • NM_007171.4:c.1318G>A
  • NP_001070833.1:p.Ala418Thr
  • NP_001070834.1:p.Ala364Thr
  • NP_001129585.1:p.Ala418Thr
  • NP_001129586.1:p.Ala301Thr
  • NP_001340122.2:p.Ala440Thr
  • NP_001340123.1:p.Ala364Thr
  • NP_001340124.1:p.Ala301Thr
  • NP_001340125.1:p.Ala388Thr
  • NP_001340126.2:p.Ala386Thr
  • NP_001340127.2:p.Ala386Thr
  • NP_001340128.2:p.Ala323Thr
  • NP_001340129.1:p.Ala266Thr
  • NP_001361618.1:p.Ala414Thr
  • NP_001361619.1:p.Ala418Thr
  • NP_001361620.1:p.Ala301Thr
  • NP_001361621.1:p.Ala301Thr
  • NP_001361622.1:p.Ala301Thr
  • NP_001361624.1:p.Ala288Thr
  • NP_009102.3:p.Ala440Thr
  • NP_009102.4:p.Ala440Thr
  • LRG_842t1:c.1318G>A
  • LRG_842t2:c.1252G>A
  • LRG_842p1:p.Ala440Thr
  • LRG_842p2:p.Ala418Thr
  • NC_000009.11:g.134390889G>A
  • NM_007171.3:c.1318G>A
  • NR_148391.2:n.1286G>A
  • NR_148392.2:n.1504G>A
  • NR_148393.2:n.1286G>A
  • NR_148394.2:n.1179G>A
  • NR_148395.2:n.1438G>A
  • NR_148396.2:n.1072G>A
  • NR_148397.2:n.1336G>A
  • NR_148398.2:n.1291G>A
  • NR_148399.2:n.1678G>A
  • NR_148400.2:n.1277G>A
Protein change:
A266T
Links:
dbSNP: rs142057517
NCBI 1000 Genomes Browser:
rs142057517
Molecular consequence:
  • NM_001077365.2:c.1252G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001077366.2:c.1090G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001136113.2:c.1252G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001136114.2:c.901G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353193.2:c.1318G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353194.2:c.1090G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353195.2:c.901G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353196.2:c.1162G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353197.2:c.1156G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353198.2:c.1156G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353199.2:c.967G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353200.2:c.796G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374689.1:c.1240G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374690.1:c.1252G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374691.1:c.901G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374692.1:c.901G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374693.1:c.901G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374695.1:c.862G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_007171.4:c.1318G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NR_148391.2:n.1286G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148392.2:n.1504G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148393.2:n.1286G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148394.2:n.1179G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148395.2:n.1438G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148396.2:n.1072G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148397.2:n.1336G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148398.2:n.1291G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148399.2:n.1678G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148400.2:n.1277G>A - 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
SCV001416479Invitaecriteria provided, single submitter
Uncertain significance
(Mar 18, 2020)
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

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV001416479.2

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

Description

This sequence change replaces alanine with threonine at codon 440 of the POMT1 protein (p.Ala440Thr). The alanine residue is moderately conserved and there is a small physicochemical difference between alanine and threonine. This variant is present in population databases (rs142057517, ExAC 0.02%). This variant has not been reported in the literature in individuals with POMT1-related conditions. ClinVar contains an entry for this variant (Variation ID: 166896). 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 tolerated, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. 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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