NM_020297.4(ABCC9):c.878T>C (p.Phe293Ser) AND Hypertrichotic osteochondrodysplasia Cantu type

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Jun 3, 2015
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:: RCV000408624.9

Allele description [Variation Report for NM_020297.4(ABCC9):c.878T>C (p.Phe293Ser)]

NM_020297.4(ABCC9):c.878T>C (p.Phe293Ser)

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.878T>C (p.Phe293Ser)

HGVS:

NC_000012.12:g.21913005A>G
NG_012819.1:g.28690T>C
NM_001377273.1:c.878T>C
NM_001377274.1:c.14T>C
NM_005691.4:c.878T>C
NM_020297.4:c.878T>CMANE SELECT
NP_001364202.1:p.Phe293Ser
NP_001364203.1:p.Phe5Ser
NP_005682.2:p.Phe293Ser
NP_005682.2:p.Phe293Ser
NP_064693.2:p.Phe293Ser
LRG_377:g.28690T>C
NC_000012.11:g.22065939A>G
NM_005691.3:c.878T>C

Protein change:

F293S

Links:

dbSNP: rs1057516044

NCBI 1000 Genomes Browser:

rs1057516044

Molecular consequence:

NM_001377273.1:c.878T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001377274.1:c.14T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_005691.4:c.878T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_020297.4:c.878T>C - missense variant - [Sequence Ontology: SO:0001583]

Observations:

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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000484441	Victorian Clinical Genetics Services, Murdoch Childrens Research Institute	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Jun 3, 2015)	de novo	clinical testing	PubMed (2) [See all records that cite these PMIDs] 25741868, 26938784

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000484441

Victorian Clinical Genetics Services, Murdoch Childrens Research Institute

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Jun 3, 2015)

de novo

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	de novo	yes	1	1	not provided	3	yes	clinical 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

A prospective evaluation of whole-exome sequencing as a first-tier molecular test in infants with suspected monogenic disorders.

Stark Z, Tan TY, Chong B, Brett GR, Yap P, Walsh M, Yeung A, Peters H, Mordaunt D, Cowie S, Amor DJ, Savarirayan R, McGillivray G, Downie L, Ekert PG, Theda C, James PA, Yaplito-Lee J, Ryan MM, Leventer RJ, Creed E, Macciocca I, et al.

Genet Med. 2016 Nov;18(11):1090-1096. doi: 10.1038/gim.2016.1. Epub 2016 Mar 3.

PubMed [citation]

PMID:: 26938784

Details of each submission

From Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, SCV000484441.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	yes	clinical testing	PubMed (2)

Description

This change results in a substitution of a phenylalanine for a serine at amino acid position 293, NP_005682.2(ABCC9): p.(Phe293Ser). The phenylalanine is predicted to be situated just prior to the first transmembrane domain of the ABCC9 protein. The amino acid residue is highly conserved and in-silico software predicts the variant to be pathogenic. This is a novel variant, not present in population or disease databses. It was found to have occurred de novo in a child with phenotypic features of Cantu syndrome.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	de novo	yes	3	Blood	not provided		1	not provided	1	not provided

Last Updated: Oct 13, 2024

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