NM_013382.7(POMT2):c.2197C>T (p.Gln733Ter) AND multiple conditions

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Apr 30, 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:: RCV002532611.2

Allele description [Variation Report for NM_013382.7(POMT2):c.2197C>T (p.Gln733Ter)]

NM_013382.7(POMT2):c.2197C>T (p.Gln733Ter)

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.2197C>T (p.Gln733Ter)

HGVS:

NC_000014.9:g.77277432G>A
NG_008897.1:g.48451C>T
NM_013382.7:c.2197C>TMANE SELECT
NP_037514.2:p.Gln733Ter
NP_037514.2:p.Gln733Ter
LRG_844t1:c.2197C>T
LRG_844:g.48451C>T
LRG_844p1:p.Gln733Ter
NC_000014.8:g.77743775G>A
NM_013382.5:c.2197C>T

Protein change:

Q733*

Links:

dbSNP: rs1452558347

NCBI 1000 Genomes Browser:

rs1452558347

Molecular consequence:

NM_013382.7:c.2197C>T - nonsense - [Sequence Ontology: SO:0001587]

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

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003448868	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Apr 30, 2023)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 17634419, 17869517, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003448868

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Apr 30, 2023)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

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

Protein O-mannosyltransferase activities in lymphoblasts from patients with alpha-dystroglycanopathies.

Manya H, Bouchet C, Yanagisawa A, Vuillaumier-Barrot S, Quijano-Roy S, Suzuki Y, Maugenre S, Richard P, Inazu T, Merlini L, Romero NB, Leturcq F, Bezier I, Topaloglu H, Estournet B, Seta N, Endo T, Guicheney P.

Neuromuscul Disord. 2008 Jan;18(1):45-51. Epub 2007 Sep 14.

PubMed [citation]

PMID:: 17869517

See all PubMed Citations (3)

Details of each submission

From Invitae, SCV003448868.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This variant is present in population databases (no rsID available, gnomAD 0.006%). For these reasons, this variant has been classified as Pathogenic. This variant disrupts a region of the POMT2 protein in which other variant(s) (p.Trp748Arg) have been determined to be pathogenic (PMID: 17634419, 17869517). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. ClinVar contains an entry for this variant (Variation ID: 501676). This variant has not been reported in the literature in individuals affected with POMT2-related conditions. This sequence change creates a premature translational stop signal (p.Gln733*) in the POMT2 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 18 amino acid(s) of the POMT2 protein.

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

Last Updated: Mar 5, 2024

ClinVar

Relating variation to medicine