NM_013382.7(POMT2):c.1282_1284del (p.His428del) AND multiple conditions

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 3, 2018
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:: RCV000805132.7

Allele description [Variation Report for NM_013382.7(POMT2):c.1282_1284del (p.His428del)]

NM_013382.7(POMT2):c.1282_1284del (p.His428del)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

14q24.3

Genomic location:

Preferred name:

NM_013382.7(POMT2):c.1282_1284del (p.His428del)

HGVS:

NC_000014.9:g.77286794_77286796del
NG_008897.1:g.39089_39091del
NM_013382.7:c.1282_1284delMANE SELECT
NP_037514.2:p.His428del
LRG_844:g.39089_39091del
NC_000014.8:g.77753135_77753137del
NC_000014.8:g.77753137_77753139del
NM_013382.5:c.1282_1284delCAT

Protein change:

H428del

Links:

dbSNP: rs1594890912

NCBI 1000 Genomes Browser:

rs1594890912

Molecular consequence:

NM_013382.7:c.1282_1284del - inframe_deletion - [Sequence Ontology: SO:0001822]

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

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adapter molecule crk, putative [Schistosoma mansoni]
adapter molecule crk, putative [Schistosoma mansoni]
gi|1084310309|ref|XP_018646302.1|

Protein
LOC109529658 [Hippocampus comes]
LOC109529658 [Hippocampus comes]
Gene ID:109529658

Gene
Rattus norvegicus strain BN/NHsdMcwi chromosome 13, GRCr8, whole genome shotgun ...
Rattus norvegicus strain BN/NHsdMcwi chromosome 13, GRCr8, whole genome shotgun sequence
gi|2671914592|gnl|ASM:GCF_036323745 3|ref|NC_086031.1||gpp|GPC_000020856.1||gnl|NCBI_GENOMES|157502

Nucleotide
hypothetical protein ACR57_22375 [Bacillus subtilis]
hypothetical protein ACR57_22375 [Bacillus subtilis]
gi|906388949|gb|KNB75703.1||gnl|WGS |ACR57_22375

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000945077	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Dec 3, 2018)	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

SCV000945077

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Dec 3, 2018)

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, SCV000945077.4

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

Description

Experimental studies and prediction algorithms are not available for this variant, and the functional significance of the affected amino acid(s) is currently unknown. This variant has not been reported in the literature in individuals with POMT2-related conditions. This variant is not present in population databases (ExAC no frequency). This variant, c.1282_1284delCAT, results in the deletion of 1 amino acid(s) of the POMT2 protein (p.His428del), but otherwise preserves the integrity of the reading frame. 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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