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NM_032237.5(POMK):c.183G>C (p.Arg61Ser) AND multiple conditions

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Feb 11, 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:
RCV002026232.5

Allele description [Variation Report for NM_032237.5(POMK):c.183G>C (p.Arg61Ser)]

NM_032237.5(POMK):c.183G>C (p.Arg61Ser)

Gene:
POMK:protein O-mannose kinase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
8p11.21
Genomic location:
Preferred name:
NM_032237.5(POMK):c.183G>C (p.Arg61Ser)
HGVS:
  • NC_000008.11:g.43103731G>C
  • NG_033235.1:g.15226G>C
  • NM_001277971.2:c.183G>C
  • NM_032237.3:c.183G>C
  • NM_032237.5:c.183G>CMANE SELECT
  • NP_001264900.1:p.Arg61Ser
  • NP_115613.1:p.Arg61Ser
  • NC_000008.10:g.42958874G>C
Protein change:
R61S
Links:
dbSNP: rs778749095
NCBI 1000 Genomes Browser:
rs778749095
Molecular consequence:
  • NM_001277971.2:c.183G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_032237.5:c.183G>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 12 (MDDGA12)
Synonyms:
WALKER-WARBURG SYNDROME OR MUSCLE-EYE-BRAIN DISEASE, POMK-RELATED
Identifiers:
MONDO: MONDO:0014101; MedGen: C3808964; Orphanet: 899; OMIM: 615249
Name:
Limb-girdle muscular dystrophy due to POMK deficiency
Synonyms:
MUSCULAR DYSTROPHY-DYSTROGLYCANOPATHY, LIMB-GIRDLE, POMK-RELATED; Muscular dystrophy-dystroglycanopathy (limb-girdle), type c, 12
Identifiers:
MONDO: MONDO:0014489; MedGen: C4015184; Orphanet: 445110; OMIM: 616094

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002302470Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Feb 11, 2022) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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, SCV002302470.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

This sequence change replaces arginine, which is basic and polar, with serine, which is neutral and polar, at codon 61 of the POMK protein (p.Arg61Ser). This variant is present in population databases (rs778749095, gnomAD 0.009%). This variant has not been reported in the literature in individuals affected with POMK-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The serine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. 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.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024