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NM_013382.7(POMT2):c.1997A>G (p.Tyr666Cys) AND multiple conditions

Germline classification:
Pathogenic (2 submissions)
Last evaluated:
Sep 23, 2024
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000648175.18

Allele description [Variation Report for NM_013382.7(POMT2):c.1997A>G (p.Tyr666Cys)]

NM_013382.7(POMT2):c.1997A>G (p.Tyr666Cys)

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.1997A>G (p.Tyr666Cys)
Other names:
Y666C; p.Y666C:TAC>TGC; NM_013382.5(POMT2):c.1997A>G(p.Tyr666Cys)
HGVS:
  • NC_000014.9:g.77278764T>C
  • NG_008897.1:g.47119A>G
  • NM_013382.7:c.1997A>GMANE SELECT
  • NP_037514.2:p.Tyr666Cys
  • NP_037514.2:p.Tyr666Cys
  • LRG_844t1:c.1997A>G
  • LRG_844:g.47119A>G
  • LRG_844p1:p.Tyr666Cys
  • NC_000014.8:g.77745107T>C
  • NM_013382.5:c.1997A>G
  • Q9UKY4:p.Tyr666Cys
Protein change:
TYR666CYS
Links:
UniProtKB: Q9UKY4#VAR_065045; OMIM: 607439.0004; dbSNP: rs200198778
NCBI 1000 Genomes Browser:
rs200198778
Molecular consequence:
  • NM_013382.7:c.1997A>G - 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
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; 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
SCV000611299Fulgent Genetics, Fulgent Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenic
(Apr 16, 2024) 		germlineclinical testing

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

SCV000769989Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Sep 23, 2024) 		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

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

New POMT2 mutations causing congenital muscular dystrophy: identification of a founder mutation.

Yanagisawa A, Bouchet C, Van den Bergh PY, Cuisset JM, Viollet L, Leturcq F, Romero NB, Quijano-Roy S, Fardeau M, Seta N, Guicheney P.

Neurology. 2007 Sep 18;69(12):1254-60. Epub 2007 Jul 18.

PubMed [citation]
PMID:
17634419
See all PubMed Citations (5)

Details of each submission

From Fulgent Genetics, Fulgent Genetics, SCV000611299.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000769989.9

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

Description

This sequence change replaces tyrosine, which is neutral and polar, with cysteine, which is neutral and slightly polar, at codon 666 of the POMT2 protein (p.Tyr666Cys). This variant is present in population databases (rs200198778, gnomAD 0.02%). This missense change has been observed in individuals with congenital muscular dystrophy (PMID: 17634419, 17878297, 24002165). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 3221). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is expected to disrupt POMT2 protein function with a positive predictive value of 80%. For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Jun 14, 2025