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NM_001077365.2(POMT1):c.868C>T (p.Arg290Trp) AND multiple conditions

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Apr 23, 2019
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:
RCV000648159.3

Allele description

NM_001077365.2(POMT1):c.868C>T (p.Arg290Trp)

Gene:
POMT1:protein O-mannosyltransferase 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
9q34.13
Genomic location:
Preferred name:
NM_001077365.2(POMT1):c.868C>T (p.Arg290Trp)
HGVS:
  • NC_000009.12:g.131511349C>T
  • NG_008896.1:g.13448C>T
  • NM_001077365.2:c.868C>TMANE SELECT
  • NM_001077366.2:c.706C>T
  • NM_001136113.2:c.868C>T
  • NM_001136114.2:c.517C>T
  • NM_001353193.2:c.934C>T
  • NM_001353194.2:c.706C>T
  • NM_001353195.2:c.517C>T
  • NM_001353196.2:c.778C>T
  • NM_001353197.2:c.772C>T
  • NM_001353198.2:c.772C>T
  • NM_001353199.2:c.583C>T
  • NM_001353200.2:c.412C>T
  • NM_001374689.1:c.851C>T
  • NM_001374690.1:c.868C>T
  • NM_001374691.1:c.517C>T
  • NM_001374692.1:c.517C>T
  • NM_001374693.1:c.706C>T
  • NM_001374695.1:c.478C>T
  • NM_007171.4:c.934C>T
  • NP_001070833.1:p.Arg290Trp
  • NP_001070834.1:p.Arg236Trp
  • NP_001129585.1:p.Arg290Trp
  • NP_001129586.1:p.Arg173Trp
  • NP_001340122.2:p.Arg312Trp
  • NP_001340123.1:p.Arg236Trp
  • NP_001340124.1:p.Arg173Trp
  • NP_001340125.1:p.Arg260Trp
  • NP_001340126.2:p.Arg258Trp
  • NP_001340127.2:p.Arg258Trp
  • NP_001340128.2:p.Arg195Trp
  • NP_001340129.1:p.Arg138Trp
  • NP_001361618.1:p.Ser284Leu
  • NP_001361619.1:p.Arg290Trp
  • NP_001361620.1:p.Arg173Trp
  • NP_001361621.1:p.Arg173Trp
  • NP_001361622.1:p.Arg236Trp
  • NP_001361624.1:p.Arg160Trp
  • NP_009102.3:p.Arg312Trp
  • NP_009102.4:p.Arg312Trp
  • LRG_842t1:c.934C>T
  • LRG_842t2:c.868C>T
  • LRG_842p1:p.Arg312Trp
  • LRG_842p2:p.Arg290Trp
  • NC_000009.11:g.134386736C>T
  • NM_007171.3:c.934C>T
  • NR_148391.2:n.902C>T
  • NR_148392.2:n.1120C>T
  • NR_148393.2:n.902C>T
  • NR_148394.2:n.790C>T
  • NR_148395.2:n.1054C>T
  • NR_148396.2:n.683C>T
  • NR_148397.2:n.947C>T
  • NR_148398.2:n.902C>T
  • NR_148399.2:n.1294C>T
  • NR_148400.2:n.888C>T
Protein change:
R138W
Links:
dbSNP: rs886042627
NCBI 1000 Genomes Browser:
rs886042627
Molecular consequence:
  • NM_001077365.2:c.868C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001077366.2:c.706C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001136113.2:c.868C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001136114.2:c.517C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353193.2:c.934C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353194.2:c.706C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353195.2:c.517C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353196.2:c.778C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353197.2:c.772C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353198.2:c.772C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353199.2:c.583C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353200.2:c.412C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374689.1:c.851C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374690.1:c.868C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374691.1:c.517C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374692.1:c.517C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374693.1:c.706C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374695.1:c.478C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_007171.4:c.934C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_148391.2:n.902C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148392.2:n.1120C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148393.2:n.902C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148394.2:n.790C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148395.2:n.1054C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148396.2:n.683C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148397.2:n.947C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148398.2:n.902C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148399.2:n.1294C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148400.2:n.888C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
Autosomal recessive limb-girdle muscular dystrophy type 2K
Synonyms:
MUSCULAR DYSTROPHY-DYSTROGLYCANOPATHY (LIMB-GIRDLE), TYPE C, 1; MUSCULAR DYSTROPHY, LIMB-GIRDLE, TYPE 2K; Limb-girdle muscular dystrophy-dystroglycanopathy, type C1; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0012248; MedGen: C1836373; Orphanet: 86812; OMIM: 609308
Name:
Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B1 (MDDGB1)
Synonyms:
MUSCULAR DYSTROPHY, CONGENITAL, POMT1-RELATED; MUSCULAR DYSTROPHY-DYSTROGLYCANOPATHY (CONGENITAL WITH IMPAIRED INTELLECTUAL IMPAIRMENT), TYPE B, 1
Identifiers:
MONDO: MONDO:0013159; MedGen: C3150415; OMIM: 613155
Name:
Walker-Warburg congenital muscular dystrophy (MDDGA1)
Synonyms:
HARD syndrome; Muscular dystrophy-dystroglycanopathy, type A; Walker-Warburg syndrome
Identifiers:
MONDO: MONDO:0000171; MedGen: C0265221; Orphanet: 899; OMIM: PS236670

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000769973Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Apr 23, 2019) 		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):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV000769973.3

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

Description

This sequence change replaces arginine with tryptophan at codon 312 of the POMT1 protein (p.Arg312Trp). The arginine residue is highly conserved and there is a moderate physicochemical difference between arginine and tryptophan. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with POMT1-related disease. ClinVar contains an entry for this variant (Variation ID: 283451). Algorithms developed to predict the effect of missense changes on protein structure and function do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C15"). 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: Apr 23, 2022