NM_001077365.2(POMT1):c.389A>C (p.His130Pro) AND multiple conditions

Clinical significance:Uncertain significance (Last evaluated: Nov 10, 2017)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000527153.2

Allele description [Variation Report for NM_001077365.2(POMT1):c.389A>C (p.His130Pro)]

NM_001077365.2(POMT1):c.389A>C (p.His130Pro)

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.389A>C (p.His130Pro)
HGVS:
  • NC_000009.12:g.131507476A>C
  • NG_008896.1:g.9575A>C
  • NM_001077365.2:c.389A>CMANE SELECT
  • NM_001077366.2:c.227A>C
  • NM_001136113.2:c.389A>C
  • NM_001136114.2:c.38A>C
  • NM_001353193.2:c.389A>C
  • NM_001353194.2:c.227A>C
  • NM_001353195.2:c.38A>C
  • NM_001353196.2:c.299A>C
  • NM_001353197.2:c.227A>C
  • NM_001353198.2:c.227A>C
  • NM_001353199.2:c.38A>C
  • NM_001353200.2:c.-30+1023A>C
  • NM_001374689.1:c.227A>C
  • NM_001374690.1:c.389A>C
  • NM_001374691.1:c.38A>C
  • NM_001374692.1:c.38A>C
  • NM_001374693.1:c.227A>C
  • NM_001374695.1:c.-29-1435A>C
  • NM_007171.3:c.389A>C
  • NM_007171.4:c.389A>C
  • NP_001070833.1:p.His130Pro
  • NP_001070834.1:p.His76Pro
  • NP_001129585.1:p.His130Pro
  • NP_001129586.1:p.His13Pro
  • NP_001340122.2:p.His130Pro
  • NP_001340123.1:p.His76Pro
  • NP_001340124.1:p.His13Pro
  • NP_001340125.1:p.His100Pro
  • NP_001340126.2:p.His76Pro
  • NP_001340127.2:p.His76Pro
  • NP_001340128.2:p.His13Pro
  • NP_001361618.1:p.His76Pro
  • NP_001361619.1:p.His130Pro
  • NP_001361620.1:p.His13Pro
  • NP_001361621.1:p.His13Pro
  • NP_001361622.1:p.His76Pro
  • NP_009102.3:p.His130Pro
  • NP_009102.4:p.His130Pro
  • LRG_842t1:c.389A>C
  • LRG_842t2:c.389A>C
  • LRG_842p1:p.His130Pro
  • LRG_842p2:p.His130Pro
  • NC_000009.11:g.134382863A>C
  • NR_148391.2:n.423A>C
  • NR_148392.2:n.575A>C
  • NR_148393.2:n.423A>C
  • NR_148394.2:n.423A>C
  • NR_148395.2:n.575A>C
  • NR_148396.2:n.316A>C
  • NR_148397.2:n.468A>C
  • NR_148398.2:n.423A>C
  • NR_148399.2:n.815A>C
Protein change:
H100P
Links:
dbSNP: rs752880907
NCBI 1000 Genomes Browser:
rs752880907
Molecular consequence:
  • NM_001353200.2:c.-30+1023A>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001374695.1:c.-29-1435A>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001077365.2:c.389A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001077366.2:c.227A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001136113.2:c.389A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001136114.2:c.38A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353193.2:c.389A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353194.2:c.227A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353195.2:c.38A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353196.2:c.299A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353197.2:c.227A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353198.2:c.227A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353199.2:c.38A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374689.1:c.227A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374690.1:c.389A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374691.1:c.38A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374692.1:c.38A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374693.1:c.227A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_007171.3:c.389A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_007171.4:c.389A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NR_148391.2:n.423A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148392.2:n.575A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148393.2:n.423A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148394.2:n.423A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148395.2:n.575A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148396.2:n.316A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148397.2:n.468A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148398.2:n.423A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148399.2:n.815A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
Limb-girdle muscular dystrophy-dystroglycanopathy, type C1 (MDDGC1)
Synonyms:
MUSCULAR DYSTROPHY-DYSTROGLYCANOPATHY (LIMB-GIRDLE), TYPE C, 1; MUSCULAR DYSTROPHY, LIMB-GIRDLE, TYPE 2K; MUSCULAR DYSTROPHY, LIMB-GIRDLE, AUTOSOMAL RECESSIVE 11
Identifiers:
MONDO: MONDO:0012248; MedGen: C1836373; Orphanet: 86812; OMIM: 609308
Name:
Congenital muscular dystrophy-dystroglycanopathy with mental retardation, type B1 (MDDGB1)
Synonyms:
MUSCULAR DYSTROPHY, CONGENITAL, POMT1-RELATED; MUSCULAR DYSTROPHY-DYSTROGLYCANOPATHY (CONGENITAL WITH IMPAIRED INTELLECTUAL IMPAIRMENT), TYPE B, 1; Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B1
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

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000649900Invitaecriteria provided, single submitter
Uncertain significance
(Nov 10, 2017)
germlineclinical testing

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

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, SCV000649900.2

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

Description

This sequence change replaces histidine with proline at codon 130 of the POMT1 protein (p.His130Pro). The histidine residue is moderately conserved and there is a moderate physicochemical difference between histidine and proline. This variant is present in population databases (rs752880907, ExAC 0.009%). This variant has not been reported in the literature in individuals with POMT1-related disease. 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 proline amino acid residue is found in multiple mammalian species, suggesting that this missense change does not adversely affect protein function. These predictions have not been confirmed by published functional studies and their clinical significance is uncertain. 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: Jun 14, 2021

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