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NM_013382.7(POMT2):c.1261C>T (p.Arg421Trp) AND Autosomal recessive limb-girdle muscular dystrophy

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Sep 21, 2021
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:
RCV001731484.1

Allele description [Variation Report for NM_013382.7(POMT2):c.1261C>T (p.Arg421Trp)]

NM_013382.7(POMT2):c.1261C>T (p.Arg421Trp)

Gene:
POMT2:protein O-mannosyltransferase 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
14q24.3
Genomic location:
Preferred name:
NM_013382.7(POMT2):c.1261C>T (p.Arg421Trp)
HGVS:
  • NC_000014.9:g.77286815G>A
  • NG_008897.1:g.39068C>T
  • NM_013382.7:c.1261C>TMANE SELECT
  • NP_037514.2:p.Arg421Trp
  • NP_037514.2:p.Arg421Trp
  • LRG_844t1:c.1261C>T
  • LRG_844:g.39068C>T
  • LRG_844p1:p.Arg421Trp
  • NC_000014.8:g.77753158G>A
  • NM_013382.5:c.1261C>T
  • p.Arg421Trp
Protein change:
R421W
Links:
dbSNP: rs727502855
NCBI 1000 Genomes Browser:
rs727502855
Molecular consequence:
  • NM_013382.7:c.1261C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Autosomal recessive limb-girdle muscular dystrophy
Identifiers:
MONDO: MONDO:0015152; MedGen: C2931907; OMIM: PS253600

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001983638Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Likely pathogenic
(Sep 21, 2021) 		germlineclinical testing

PubMed (4)
[See all records that cite these PMIDs]

Citation Link

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Summary from all submissions

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

Citations

PubMed

Detection of variants in dystroglycanopathy-associated genes through the application of targeted whole-exome sequencing analysis to a large cohort of patients with unexplained limb-girdle muscle weakness.

Johnson K, Bertoli M, Phillips L, Töpf A, Van den Bergh P, Vissing J, Witting N, Nafissi S, Jamal-Omidi S, Łusakowska A, Kostera-Pruszczyk A, Potulska-Chromik A, Deconinck N, Wallgren-Pettersson C, Strang-Karlsson S, Colomer J, Claeys KG, De Ridder W, Baets J, von der Hagen M, Fernández-Torrón R, Zulaica Ijurco M, et al.

Skelet Muscle. 2018 Jul 30;8(1):23. doi: 10.1186/s13395-018-0170-1.

PubMed [citation]
PMID:
30060766
PMCID:
PMC6066920

Genetic variations and clinical spectrum of dystroglycanopathy in a large cohort of Chinese patients.

Song D, Dai Y, Chen X, Fu X, Chang X, Wang N, Zhang C, Yan C, Zheng H, Wu L, Jiang L, Hua Y, Yang H, Wang Z, Dai T, Zhu W, Han C, Yuan Y, Kobayashi K, Toda T, Xiong H.

Clin Genet. 2021 Mar;99(3):384-395. doi: 10.1111/cge.13886. Epub 2021 Jan 19.

PubMed [citation]
PMID:
33200426
See all PubMed Citations (4)

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV001983638.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (4)

Description

Variant summary: POMT2 c.1261C>T (p.Arg421Trp) results in a non-conservative amino acid change located in the MIR motif domain (IPR016093) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 2.4e-05 in 251482 control chromosomes. c.1261C>T has been reported in the literature as a compound heterozygous genotype in comprehensively genotyped (WES/panel based analysis) and well phenotyped set of individuals affected with Autosomal Recessive Limb-Girdle Muscular Dystrophy and has been subsequently cited by others (example, Johnson_2018, Ostergaard_2018, Topf_2020, Song_2021). These data indicate that the variant is likely to be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Three clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as likely pathogenic.

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

Last Updated: Apr 13, 2025