NM_013382.7(POMT2):c.1261C>T (p.Arg421Trp) AND multiple conditions

Germline classification:: Likely pathogenic (2 submissions)
Last evaluated:: Nov 5, 2024
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000699248.9

Allele description [Variation Report for NM_013382.7(POMT2):c.1261C>T (p.Arg421Trp)]

NM_013382.7(POMT2):c.1261C>T (p.Arg421Trp)

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.1261C>T (p.Arg421Trp)

HGVS:

NC_000014.9:g.77286815G>A
NG_008897.1:g.39068C>T
NM_013382.7:c.1261C>TMANE SELECT
NP_037514.2:p.Arg421Trp
NP_037514.2:p.Arg421Trp
LRG_844t1:c.1261C>T
LRG_844:g.39068C>T
LRG_844p1:p.Arg421Trp
NC_000014.8:g.77753158G>A
NM_013382.5:c.1261C>T
p.Arg421Trp

Protein change:

R421W

Links:

dbSNP: rs727502855

NCBI 1000 Genomes Browser:

rs727502855

Molecular consequence:

NM_013382.7:c.1261C>T - 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
SCV000827950	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely pathogenic (Nov 5, 2024)	germline	clinical testing	PubMed (6) [See all records that cite these PMIDs] 27854218, 30060766, 31127727, 33200426, 34413876, 28492532
SCV002811469	Fulgent Genetics, Fulgent Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Jun 4, 2024)	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

SCV000827950

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely pathogenic
(Nov 5, 2024)

germline

clinical testing

PubMed (6)
[See all records that cite these PMIDs]

SCV002811469

Fulgent Genetics, Fulgent Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Jun 4, 2024)

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

Targeted Re-Sequencing Emulsion PCR Panel for Myopathies: Results in 94 Cases.

Punetha J, Kesari A, Uapinyoying P, Giri M, Clarke NF, Waddell LB, North KN, Ghaoui R, O'Grady GL, Oates EC, Sandaradura SA, Bönnemann CG, Donkervoort S, Plotz PH, Smith EC, Tesi-Rocha C, Bertorini TE, Tarnopolsky MA, Reitter B, Hausmanowa-Petrusewicz I, Hoffman EP.

J Neuromuscul Dis. 2016 May 27;3(2):209-225.

PubMed [citation]

PMID:: 27854218

Detection of variants in dystroglycanopathy-associated genes through the application of targeted whole-exome sequencing analysis to a large cohort of patients with unexplained limb-girdle muscle weakness.

Johnson K, Bertoli M, Phillips L, Töpf A, Van den Bergh P, Vissing J, Witting N, Nafissi S, Jamal-Omidi S, Łusakowska A, Kostera-Pruszczyk A, Potulska-Chromik A, Deconinck N, Wallgren-Pettersson C, Strang-Karlsson S, Colomer J, Claeys KG, De Ridder W, Baets J, von der Hagen M, Fernández-Torrón R, Zulaica Ijurco M, et al.

Skelet Muscle. 2018 Jul 30;8(1):23. doi: 10.1186/s13395-018-0170-1.

PubMed [citation]

PMID:: 30060766
PMCID:: PMC6066920

See all PubMed Citations (7)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000827950.7

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (6)

Description

This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 421 of the POMT2 protein (p.Arg421Trp). This variant is present in population databases (rs727502855, gnomAD 0.01%). This missense change has been observed in individuals with clinical features of POMT2-related conditions (PMID: 27854218, 30060766, 31127727, 33200426, 34413876). ClinVar contains an entry for this variant (Variation ID: 162597). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed for this missense variant. However, the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on POMT2 protein function. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.

#	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

From Fulgent Genetics, Fulgent Genetics, SCV002811469.2

#	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	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Apr 13, 2025

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