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NM_013382.7(POMT2):c.1997A>G (p.Tyr666Cys) AND Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B2

Germline classification:
Likely pathogenic (3 submissions)
Last evaluated:
May 31, 2018
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:
RCV000003376.18

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 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

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000023534OMIM
no assertion criteria provided
Pathogenic
(Jul 1, 2009)
germlineliterature only

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

SCV000265767Center for Genetic Medicine Research, Children's National Medical Center
criteria provided, single submitter

(Punetha et al. (J Neuromuscul Dis. 2016))
Likely pathogenic
(Dec 1, 2015)
unknownresearch

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

SCV000803551SIB Swiss Institute of Bioinformatics
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenic
(May 31, 2018)
unknowncuration

PubMed (5)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only
not providedunknownyesnot providednot providednot providednot providednot providedresearch
not providedunknownunknownnot providednot providednot providednot providednot providedcuration

Citations

PubMed

Targeted Re-Sequencing Emulsion PCR Panel for Myopathies: Results in 94 Cases.

Punetha J, Kesari A, Uapinyoying P, Giri M, Clarke NF, Waddell LB, North KN, Ghaoui R, O'Grady GL, Oates EC, Sandaradura SA, Bönnemann CG, Donkervoort S, Plotz PH, Smith EC, Tesi-Rocha C, Bertorini TE, Tarnopolsky MA, Reitter B, Hausmanowa-Petrusewicz I, Hoffman EP.

J Neuromuscul Dis. 2016 May 27;3(2):209-225.

PubMed [citation]
PMID:
27854218

Refining genotype phenotype correlations in muscular dystrophies with defective glycosylation of dystroglycan.

Godfrey C, Clement E, Mein R, Brockington M, Smith J, Talim B, Straub V, Robb S, Quinlivan R, Feng L, Jimenez-Mallebrera C, Mercuri E, Manzur AY, Kinali M, Torelli S, Brown SC, Sewry CA, Bushby K, Topaloglu H, North K, Abbs S, Muntoni F.

Brain. 2007 Oct;130(Pt 10):2725-35. Epub 2007 Sep 18.

PubMed [citation]
PMID:
17878207
See all PubMed Citations (6)

Details of each submission

From OMIM, SCV000023534.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (4)

Description

In 2 unrelated patients with congenital muscular dystrophy and severe mental retardation (MDDGB2; 613156), Yanagisawa et al. (2007) identified a homozygous 1997A-G transition in exon 19 of the POMT2 gene, resulting in a tyr666-to-cys (Y666C) substitution in a highly conserved residue. The patients were of Moroccan and French descent, respectively. Haplotype analysis indicated a founder effect. Two additional patients with a similar phenotype were compound heterozygous for Y666C and another pathogenic POMT2 mutation (W647X; 607439.0005 and W748R; 607439.0006).

Godfrey et al. (2007) identified a homozygous Y666C substitution in 2 sibs with congenital muscular dystrophy and low IQ. Both patients had onset in infancy and increased serum creatine kinase. One achieved walking, the other sitting. One had contractures, muscle hypertrophy, and microcephaly. The other had hypoplastic cerebellum, micropenis, and cryptorchidism.

Godfrey et al. (2007) identified a homozygous Y666C mutation in a patient classified as having muscle-eye-brain disease (MDDGA2; 613150). The patient, who reportedly had onset at age 4 years, never achieved walking, and had increased serum creatine kinase, muscle hypertrophy, microcephaly, low IQ, and encephalocele. Two additional patients with muscle-eye-brain disease were compound heterozygous for Y666C and another pathogenic POMT2 mutation (see, e.g., R413P; 607439.0007).

Mercuri et al. (2009) identified compound heterozygosity for Y666C and G246D (607439.0016) in an Italian patient with congenital muscular dystrophy, microcephaly, mental retardation, but normal brain MRI with minimal white matter changes.

Yanagisawa et al. (2009) reported 3 unrelated French patients who were compound heterozygous for the Y666C mutation and another pathogenic mutation in the POMT2 gene. Two patients with MDDGB2 were compound heterozygous for Y666C and another pathogenic mutation (see, e.g., 607439.0017), whereas the third had the more severe MDDGA2 phenotype and carried Y666C and a deletion of several exons of the POMT2 gene.

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

From Center for Genetic Medicine Research, Children's National Medical Center, SCV000265767.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedresearch PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot providednot providednot providednot providednot provided

From SIB Swiss Institute of Bioinformatics, SCV000803551.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcuration PubMed (5)

Description

This variant is interpreted as a Likely Pathogenic, for Muscular dystrophy-dystroglycanopathy (congenital with mental retardation), type B, 2, in Autosomal Recessive manner. The following ACMG Tag(s) were applied: PP3 => Multiple lines of computational evidence support a deleterious effect on the gene or gene product. PM3 => For recessive disorders, detected in trans with a pathogenic variant (PMID:17634419,19138766). PP1 => Cosegregation with disease in multiple affected family members in a gene definitively known to cause the disease (PMID:17878207). PM2 => Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium. PS4-Moderate => Found in multiple unrelated patients (PMID:17878207,17634419,19138766,19299310).

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

Last Updated: May 7, 2024