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NM_001077365.2(POMT1):c.752C>T (p.Pro251Leu) AND POMT1-related disorder

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Dec 1, 2023
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:
RCV004542790.1

Allele description [Variation Report for NM_001077365.2(POMT1):c.752C>T (p.Pro251Leu)]

NM_001077365.2(POMT1):c.752C>T (p.Pro251Leu)

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.752C>T (p.Pro251Leu)
HGVS:
  • NC_000009.12:g.131510312C>T
  • NG_008896.1:g.12411C>T
  • NM_001077365.2:c.752C>TMANE SELECT
  • NM_001077366.2:c.590C>T
  • NM_001136113.2:c.752C>T
  • NM_001136114.2:c.401C>T
  • NM_001353193.2:c.818C>T
  • NM_001353194.2:c.590C>T
  • NM_001353195.2:c.401C>T
  • NM_001353196.2:c.662C>T
  • NM_001353197.2:c.656C>T
  • NM_001353198.2:c.656C>T
  • NM_001353199.2:c.467C>T
  • NM_001353200.2:c.296C>T
  • NM_001374689.1:c.735C>T
  • NM_001374690.1:c.752C>T
  • NM_001374691.1:c.401C>T
  • NM_001374692.1:c.401C>T
  • NM_001374693.1:c.590C>T
  • NM_001374695.1:c.362C>T
  • NM_007171.4:c.818C>T
  • NP_001070833.1:p.Pro251Leu
  • NP_001070834.1:p.Pro197Leu
  • NP_001129585.1:p.Pro251Leu
  • NP_001129586.1:p.Pro134Leu
  • NP_001340122.2:p.Pro273Leu
  • NP_001340123.1:p.Pro197Leu
  • NP_001340124.1:p.Pro134Leu
  • NP_001340125.1:p.Pro221Leu
  • NP_001340126.2:p.Pro219Leu
  • NP_001340127.2:p.Pro219Leu
  • NP_001340128.2:p.Pro156Leu
  • NP_001340129.1:p.Pro99Leu
  • NP_001361618.1:p.Pro245=
  • NP_001361619.1:p.Pro251Leu
  • NP_001361620.1:p.Pro134Leu
  • NP_001361621.1:p.Pro134Leu
  • NP_001361622.1:p.Pro197Leu
  • NP_001361624.1:p.Pro121Leu
  • NP_009102.3:p.Pro273Leu
  • NP_009102.3:p.Pro273Leu
  • NP_009102.4:p.Pro273Leu
  • LRG_842t1:c.818C>T
  • LRG_842t2:c.752C>T
  • LRG_842p1:p.Pro273Leu
  • LRG_842p2:p.Pro251Leu
  • NC_000009.11:g.134385699C>T
  • NM_007171.3:c.818C>T
  • NR_148391.2:n.786C>T
  • NR_148392.2:n.1004C>T
  • NR_148393.2:n.786C>T
  • NR_148394.2:n.674C>T
  • NR_148395.2:n.938C>T
  • NR_148396.2:n.567C>T
  • NR_148397.2:n.831C>T
  • NR_148398.2:n.786C>T
  • NR_148399.2:n.1178C>T
  • NR_148400.2:n.772C>T
Protein change:
P121L
Links:
dbSNP: rs139660235
NCBI 1000 Genomes Browser:
rs139660235
Molecular consequence:
  • NM_001077365.2:c.752C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001077366.2:c.590C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001136113.2:c.752C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001136114.2:c.401C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353193.2:c.818C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353194.2:c.590C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353195.2:c.401C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353196.2:c.662C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353197.2:c.656C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353198.2:c.656C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353199.2:c.467C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353200.2:c.296C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374690.1:c.752C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374691.1:c.401C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374692.1:c.401C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374693.1:c.590C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374695.1:c.362C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_007171.4:c.818C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_148391.2:n.786C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148392.2:n.1004C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148393.2:n.786C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148394.2:n.674C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148395.2:n.938C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148396.2:n.567C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148397.2:n.831C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148398.2:n.786C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148399.2:n.1178C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148400.2:n.772C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_001374689.1:c.735C>T - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:
POMT1-related disorder
Synonyms:
POMT1-Related Disorders; POMT1-related condition
Identifiers:

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV004757235PreventionGenetics, part of Exact Sciences
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenic
(Dec 1, 2023)
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

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From PreventionGenetics, part of Exact Sciences, SCV004757235.1

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

Description

The POMT1 c.818C>T variant is predicted to result in the amino acid substitution p.Pro273Leu. This variant was reported in an individual with Walker-Warburg syndrome (reported as c.997C>T (p.Pro273Leu) in Table S1, Willer et al. 2012. PubMed ID: 22522420; Varagur et al. 2022. PubMed ID: 34801143). This variant was also reported in the homozygous state in a fetus with hydrocephalus and additional brain malformations (See #28697; https://assises-genetique.org/sessions-de-posters-affiches/). This variant has also been associated with limb girdle muscular dystrophies, but further information was not available (Table S2, Di Fruscio et al. 2015. PubMed ID: 25898921). Functional studies in patient-derived fibroblast cell lines suggest that this variant might affect normal protein function (reported as POMT1-WWS in Figure 5 and Table S1, Willer et al. 2012. PubMed ID: 22522420). At PreventionGenetics, we have observed the c818C>T variant in the homozygous state in an individual with hydrocephalus and another patient in the compound heterozygous state with a clear pathogenic, loss-of-function variant POMT1 variant (internal data). This variant is reported in 0.016% of alleles in individuals of African descent in gnomAD and is interpreted as uncertain significance in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/variation/95469/). We interpret this variant as likely pathogenic.

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

Last Updated: Jul 7, 2024