NM_032237.5(POMK):c.222C>G (p.Cys74Trp) AND multiple conditions

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 19, 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:: RCV002937400.3

Allele description [Variation Report for NM_032237.5(POMK):c.222C>G (p.Cys74Trp)]

NM_032237.5(POMK):c.222C>G (p.Cys74Trp)

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.222C>G (p.Cys74Trp)

HGVS:

NC_000008.11:g.43103770C>G
NG_033235.1:g.15265C>G
NM_001277971.2:c.222C>G
NM_032237.5:c.222C>GMANE SELECT
NP_001264900.1:p.Cys74Trp
NP_115613.1:p.Cys74Trp
NC_000008.10:g.42958913C>G

Protein change:

C74W

Molecular consequence:

NM_001277971.2:c.222C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_032237.5:c.222C>G - 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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lipopolysaccharide biosynthesis protein [Novosphingobium lentum]
lipopolysaccharide biosynthesis protein [Novosphingobium lentum]
gi|1056649782|ref|WP_068078273.1|

Protein
Kcnk15 potassium two pore domain channel subfamily K member 15 [Rattus norvegicu...
Kcnk15 potassium two pore domain channel subfamily K member 15 [Rattus norvegicus]
Gene ID:156873

Gene
156873[uid] AND (alive[prop]) (1)
Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003258565	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jan 19, 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

SCV003258565

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jan 19, 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, SCV003258565.2

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

Description

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. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive. This variant has not been reported in the literature in individuals affected with POMK-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.01%). This sequence change replaces cysteine, which is neutral and slightly polar, with tryptophan, which is neutral and slightly polar, at codon 74 of the POMK protein (p.Cys74Trp).

#	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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