NM_013382.7(POMT2):c.2085_2086delinsTT (p.Trp695_Pro696delinsCysSer) AND multiple conditions

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jun 1, 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:: RCV000685895.6

Allele description [Variation Report for NM_013382.7(POMT2):c.2085_2086delinsTT (p.Trp695_Pro696delinsCysSer)]

NM_013382.7(POMT2):c.2085_2086delinsTT (p.Trp695_Pro696delinsCysSer)

Gene:

POMT2:protein O-mannosyltransferase 2 [Gene - OMIM - HGNC]

Variant type:

Indel

Cytogenetic location:

14q24.3

Genomic location:

Preferred name:

NM_013382.7(POMT2):c.2085_2086delinsTT (p.Trp695_Pro696delinsCysSer)

HGVS:

NC_000014.9:g.77278455_77278456delinsAA
NG_008897.1:g.47427_47428delinsTT
NM_013382.5:c.2085_2086delinsTT
NM_013382.7:c.2085_2086delinsTTMANE SELECT
NP_037514.2:p.Trp695_Pro696delinsCysSer
LRG_844t1:c.2085_2086delinsTT
LRG_844:g.47427_47428delinsTT
NC_000014.8:g.77744798_77744799delinsAA
NM_013382.5:c.2085_2086delGCinsTT

Links:

dbSNP: rs1566642523

NCBI 1000 Genomes Browser:

rs1566642523

Molecular consequence:

NM_013382.7:c.2085_2086delinsTT - 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; 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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000813395	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jun 1, 2022)	germline	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

SCV000813395

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jun 1, 2022)

germline

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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

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 Labcorp Genetics (formerly Invitae), Labcorp, SCV000813395.3

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

Description

This variant, c.2085_2086delinsTT, is a complex sequence change that results in the deletion of 2 and insertion of 2 amino acid(s) in the POMT2 protein (p.Trp695_Pro696delinsCysSer). Information on the frequency of this variant in the gnomAD database is not available, as this variant may be reported differently in the database. This variant has not been reported in the literature in individuals affected with POMT2-related conditions. ClinVar contains an entry for this variant (Variation ID: 566152). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	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: Sep 29, 2024

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