NM_013382.7(POMT2):c.1057G>A (p.Gly353Ser) AND Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2

Germline classification:: Likely pathogenic (2 submissions)
Last evaluated:: Feb 8, 2024
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:: RCV000003387.5

Allele description [Variation Report for NM_013382.7(POMT2):c.1057G>A (p.Gly353Ser)]

NM_013382.7(POMT2):c.1057G>A (p.Gly353Ser)

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.1057G>A (p.Gly353Ser)

HGVS:

NC_000014.9:g.77296223C>T
NG_008897.1:g.29660G>A
NM_013382.7:c.1057G>AMANE SELECT
NP_037514.2:p.Gly353Ser
NP_037514.2:p.Gly353Ser
LRG_844t1:c.1057G>A
LRG_844:g.29660G>A
LRG_844p1:p.Gly353Ser
NC_000014.8:g.77762566C>T
NM_013382.5:c.1057G>A
Q9UKY4:p.Gly353Ser

Protein change:

G353S; GLY353SER

Links:

UniProtKB: Q9UKY4#VAR_065040; OMIM: 607439.0012; OMIM: 607439.0014; dbSNP: rs267606970

NCBI 1000 Genomes Browser:

rs267606970

Molecular consequence:

NM_013382.7:c.1057G>A - 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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000023545	OMIM	no assertion criteria provided	Pathogenic (Jul 1, 2006)	germline	literature only	PubMed (1) [See all records that cite this PMID]
SCV004204109	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Feb 8, 2024)	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

SCV000023545

OMIM

no assertion criteria provided

Pathogenic
(Jul 1, 2006)

germline

literature only

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

SCV004204109

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Feb 8, 2024)

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 mutation in a patient with 'MEB-like' phenotype.

Mercuri E, D'Amico A, Tessa A, Berardinelli A, Pane M, Messina S, van Reeuwijk J, Bertini E, Muntoni F, Santorelli FM.

Neuromuscul Disord. 2006 Jul;16(7):446-8. Epub 2006 May 15.

PubMed [citation]

PMID:: 16701995

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, SCV000023545.2

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

Description

In an 11-year-old Italian girl with muscle-eye-brain disease (MDDGA2; 613150), Mercuri et al. (2006) identified compound heterozygosity for 2 mutations in the POMT2 gene: a 1057G-A transition in exon 9 resulting in a gly353-to-ser (G353S) substitution, and a 2177G-A transition in exon 21 resulting in a gly726-to-glu (G726E; 607439.0013) substitution. She was found to have ventricular dilatation and hypoplasia of the cerebellar vermis on prenatal ultrasound at 28 weeks' gestation. After birth, she was hypotonic and never achieved independent sitting. She showed poor growth, respiratory insufficiency, severe mental retardation with only a few words, microcephaly, severe muscle weakness, macroglossia, contractures, and muscle hypertrophy of the lower limbs. Brain MRI showed hypoplasia of the cerebellar vermis and pons, as well as periventricular white matter abnormalities.

#	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, SCV004204109.2

#	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: May 16, 2025

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