NM_013382.7(POMT2):c.1333-14G>A AND Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2

Germline classification:: Likely pathogenic (2 submissions)
Last evaluated:: Apr 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:: RCV000003391.5

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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000023549	OMIM	no assertion criteria provided	Pathogenic (Jul 1, 2009)	germline	literature only	PubMed (1) [See all records that cite this PMID]
SCV004204127	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Apr 19, 2022)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000023549

OMIM

no assertion criteria provided

Pathogenic
(Jul 1, 2009)

germline

literature only

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

SCV004204127

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Apr 19, 2022)

unknown

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	not provided	not provided	not provided	not provided	not provided	not provided	literature only
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical 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

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

Details of each submission

From OMIM, SCV000023549.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	PubMed (1)

Description

In a 5-year-old Portuguese boy with congenital muscular dystrophy with brain and eye anomalies (MDDGA2; 613150), Yanagisawa et al. (2009) identified a homozygous G-to-A transition in intron 12 (133-14G-A) of the POMT2 gene, resulting in the creation of a new splice acceptor site and predicted to insert 4 amino acids between exons 12 and 13. In 2 sibs with MDDGA2 from an unrelated family of Argentinian descent, the authors identified compound heterozygosity for the IVS12 mutation and a 1445G-T transversion, resulting in a gly482-to-val (G482V; 607439.0019) substitution in a conserved residue in the third MIR domain. All 3 patients had microcephaly, severe mental retardation, cerebral dysplasia, cerebellar hypoplasia, and congenital hypotonia with only sitting achieved.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	not provided	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Baylor Genetics, SCV004204127.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Mar 5, 2024

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