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NM_013382.7(POMT2):c.1333-14G>A AND multiple conditions

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Dec 7, 2023
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:
RCV001851613.3

Allele description [Variation Report for NM_013382.7(POMT2):c.1333-14G>A]

NM_013382.7(POMT2):c.1333-14G>A

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.1333-14G>A
HGVS:
  • NC_000014.9:g.77285646C>T
  • NG_008897.1:g.40237G>A
  • NM_013382.7:c.1333-14G>AMANE SELECT
  • LRG_844:g.40237G>A
  • NC_000014.8:g.77751989C>T
Nucleotide change:
IVS12AS, G-A, -14
Links:
OMIM: 607439.0018; dbSNP: rs918556979
NCBI 1000 Genomes Browser:
rs918556979
Molecular consequence:
  • NM_013382.7:c.1333-14G>A - intron variant - [Sequence Ontology: SO:0001627]

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

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV002257653Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Pathogenic
(Dec 7, 2023)
germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Summary from all submissions

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

Citations

PubMed

POMT2 intragenic deletions and splicing abnormalities causing congenital muscular dystrophy with mental retardation.

Yanagisawa A, Bouchet C, Quijano-Roy S, Vuillaumier-Barrot S, Clarke N, Odent S, Rodriguez D, Romero NB, Osawa M, Endo T, Taratuto AL, Seta N, Guicheney P.

Eur J Med Genet. 2009 Jul-Aug;52(4):201-6. doi: 10.1016/j.ejmg.2008.12.004. Epub 2008 Dec 27.

PubMed [citation]
PMID:
19138766

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. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV002257653.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

This sequence change falls in intron 12 of the POMT2 gene. It does not directly change the encoded amino acid sequence of the POMT2 protein. RNA analysis indicates that this variant induces altered splicing and likely results in the gain of 4 amino acid residue(s), but is expected to preserve the integrity of the reading-frame. This variant is not present in population databases (gnomAD no frequency). This variant has been observed in individuals with clinical features of POMT2-related conditions (PMID: 19138766; Invitae). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 3235). Studies have shown that this variant results in the activation of a cryptic splice site in intron 12 (PMID: 19138766). 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: Mar 5, 2024