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NM_013382.7(POMT2):c.406T>C (p.Tyr136His) AND multiple conditions

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Aug 19, 2022
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:
RCV001367491.4

Allele description [Variation Report for NM_013382.7(POMT2):c.406T>C (p.Tyr136His)]

NM_013382.7(POMT2):c.406T>C (p.Tyr136His)

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.406T>C (p.Tyr136His)
HGVS:
  • NC_000014.9:g.77306369A>G
  • NG_008897.1:g.19514T>C
  • NM_013382.5:c.406T>C
  • NM_013382.7:c.406T>CMANE SELECT
  • NP_037514.2:p.Tyr136His
  • LRG_844t1:c.406T>C
  • LRG_844:g.19514T>C
  • NC_000014.8:g.77772712A>G
Protein change:
Y136H
Links:
dbSNP: rs1891230114
NCBI 1000 Genomes Browser:
rs1891230114
Molecular consequence:
  • NM_013382.7:c.406T>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2
Synonyms:
MUSCULAR DYSTROPHY-DYSTROGLYCANOPATHY (CONGENITAL WITH BRAIN AND EYE ANOMALIES), TYPE A, 2; WALKER-WARBURG SYNDROME OR MUSCLE-EYE-BRAIN DISEASE, POMT2-RELATED; Congenital muscular dystrophy-dystroglycanopathy with brain and eye anomalies, type A2
Identifiers:
MONDO: MONDO:0013154; MedGen: C3150411; Orphanet: 588; Orphanet: 899; OMIM: 613150
Name:
Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B2 (MDDGB2)
Synonyms:
MUSCULAR DYSTROPHY, CONGENITAL, POMT2-RELATED; MUSCULAR DYSTROPHY-DYSTROGLYCANOPATHY (CONGENITAL WITH IMPAIRED INTELLECTUAL DEVELOPMENT), TYPE B, 2
Identifiers:
MONDO: MONDO:0013160; MedGen: C3150416; OMIM: 613156
Name:
Autosomal recessive limb-girdle muscular dystrophy type 2N
Synonyms:
MUSCULAR DYSTROPHY-DYSTROGLYCANOPATHY, LIMB-GIRDLE, POMT2-RELATED; Limb-girdle muscular dystrophy-dystroglycanopathy, type C2; Muscular dystrophy-dystroglycanopathy (limb-girdle), type C, 2
Identifiers:
MONDO: MONDO:0013162; MedGen: C3150418; Orphanet: 206559; OMIM: 613158

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001563843Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Aug 19, 2022) 		germlineclinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

Limb girdle muscular dystrophy due to mutations in POMT2.

Østergaard ST, Johnson K, Stojkovic T, Krag T, De Ridder W, De Jonghe P, Baets J, Claeys KG, Fernández-Torrón R, Phillips L, Topf A, Colomer J, Nafissi S, Jamal-Omidi S, Bouchet-Seraphin C, Leturcq F, MacArthur DG, Lek M, Xu L, Nelson I, Straub V, Vissing J.

J Neurol Neurosurg Psychiatry. 2018 May;89(5):506-512. doi: 10.1136/jnnp-2017-317018. Epub 2017 Nov 24.

PubMed [citation]
PMID:
29175898

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
See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001563843.3

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

Description

This sequence change replaces tyrosine, which is neutral and polar, with histidine, which is basic and polar, at codon 136 of the POMT2 protein (p.Tyr136His). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with clinical features of POMT2-related conditions (PMID: 29175898, 30060766, 32528171). ClinVar contains an entry for this variant (Variation ID: 1058360). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). 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: Sep 29, 2024