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NM_020297.4(ABCC9):c.3605C>T (p.Thr1202Met) AND Hypertrichotic osteochondrodysplasia Cantu type

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Oct 19, 2020
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:
RCV002471162.9

Allele description [Variation Report for NM_020297.4(ABCC9):c.3605C>T (p.Thr1202Met)]

NM_020297.4(ABCC9):c.3605C>T (p.Thr1202Met)

Gene:
ABCC9:ATP binding cassette subfamily C member 9 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
12p12.1
Genomic location:
Preferred name:
NM_020297.4(ABCC9):c.3605C>T (p.Thr1202Met)
HGVS:
  • NC_000012.12:g.21829022G>A
  • NG_012819.1:g.112673C>T
  • NM_001377273.1:c.3605C>T
  • NM_001377274.1:c.2738C>T
  • NM_005691.4:c.3605C>T
  • NM_020297.4:c.3605C>TMANE SELECT
  • NP_001364202.1:p.Thr1202Met
  • NP_001364203.1:p.Thr913Met
  • NP_005682.2:p.Thr1202Met
  • NP_064693.2:p.Thr1202Met
  • LRG_377t2:c.3605C>T
  • LRG_377:g.112673C>T
  • NC_000012.11:g.21981956G>A
  • NM_005691.3:c.3605C>T
Protein change:
T1202M
Links:
dbSNP: rs2137272605
NCBI 1000 Genomes Browser:
rs2137272605
Molecular consequence:
  • NM_001377273.1:c.3605C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001377274.1:c.2738C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_005691.4:c.3605C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_020297.4:c.3605C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Hypertrichotic osteochondrodysplasia Cantu type
Synonyms:
Hypertrichotic osteochondrodysplasia; Cantu syndrome
Identifiers:
MONDO: MONDO:0009406; MedGen: C0795905; Orphanet: 1517; OMIM: 239850

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002767776Victorian Clinical Genetics Services, Murdoch Childrens Research Institute

See additional submitters

criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenic
(Oct 19, 2020) 		germlineclinical testing

PubMed (5)
[See all records that cite these PMIDs]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Dominant missense mutations in ABCC9 cause Cantú syndrome.

Harakalova M, van Harssel JJ, Terhal PA, van Lieshout S, Duran K, Renkens I, Amor DJ, Wilson LC, Kirk EP, Turner CL, Shears D, Garcia-Minaur S, Lees MM, Ross A, Venselaar H, Vriend G, Takanari H, Rook MB, van der Heyden MA, Asselbergs FW, Breur HM, Swinkels ME, et al.

Nat Genet. 2012 May 18;44(7):793-6. doi: 10.1038/ng.2324.

PubMed [citation]
PMID:
22610116

Aortic aneurysm and craniosynostosis in a family with Cantu syndrome.

Hiraki Y, Miyatake S, Hayashidani M, Nishimura Y, Matsuura H, Kamada M, Kawagoe T, Yunoki K, Okamoto N, Yofune H, Nakashima M, Tsurusaki Y, Satisu H, Murakami A, Miyake N, Nishimura G, Matsumoto N.

Am J Med Genet A. 2014 Jan;164A(1):231-6. doi: 10.1002/ajmg.a.36228. Epub 2013 Nov 25.

PubMed [citation]
PMID:
24352916
See all PubMed Citations (5)

Details of each submission

From Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, SCV002767776.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (5)

Description

Based on the classification scheme VCGS_Germline_v1.3.3, this variant is classified as Pathogenic. Following criteria are met: 0103 - Loss of function and gain of function are known mechanisms of disease in this gene. Loss of function is associated with dilated cardiomyopathy (MIM# 608569; OMIM). Gain of function is associated with Cantu syndrome (MIM#239850; PMID: 22610116). (I) 0107 - This gene is associated with autosomal dominant disease. (I) 0200 - Variant is predicted to result in a missense amino acid change from threonine to methionine. (I) 0251 - This variant is heterozygous. (I) 0301 - Variant is absent from gnomAD (both v2 and v3). (SP) 0502 - Missense variant with conflicting in silico predictions and uninformative conservation. (I) 0600 - Variant is located in the annotated ABC membrane domain (PDB). (I) 0710 – Another missense variant comparable to the one identified in this case has inconclusive previous evidence for pathogenicity. A different variant in the same codon resulting in a change to an alanine has been reported as a VUS in ClinVar. (I) 0802 - This variant has moderate previous evidence of pathogenicity in unrelated individuals. This variant has been previously reported as pathogenic in two unrelated individuals and their affected fathers with Cantu syndrome (PMID: 24352916, 31828977, 32622958). (SP) 1102 - Strong phenotype match for this individual. (SP) 1204 - This variant has been shown to be de novo in the proband (parental status not tested but assumed) (UMC Utrecht report). Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign

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

Last Updated: Nov 24, 2024