NM_173076.3(ABCA12):c.2332+2T>C AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Mar 30, 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:: RCV003672574.2

Allele description [Variation Report for NM_173076.3(ABCA12):c.2332+2T>C]

NM_173076.3(ABCA12):c.2332+2T>C

Gene:

ABCA12:ATP binding cassette subfamily A member 12 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2q35

Genomic location:

Preferred name:

NM_173076.3(ABCA12):c.2332+2T>C

HGVS:

NC_000002.12:g.215011437A>G
NG_007074.1:g.131991T>C
NG_007074.2:g.132189T>C
NM_015657.4:c.1378+2T>C
NM_173076.3:c.2332+2T>CMANE SELECT
NC_000002.11:g.215876161A>G

Molecular consequence:

NM_015657.4:c.1378+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
NM_173076.3:c.2332+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004389312	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Mar 30, 2023)	germline	clinical testing	PubMed (5) [See all records that cite these PMIDs] 22992804, 31168818, 16199547, 20672373, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004389312

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Mar 30, 2023)

germline

clinical testing

PubMed (5)
[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	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Targeted sequence capture and high-throughput sequencing in the molecular diagnosis of ichthyosis and other skin diseases.

Scott CA, Plagnol V, Nitoiu D, Bland PJ, Blaydon DC, Chronnell CM, Poon DS, Bourn D, Gárdos L, Császár A, Tihanyi M, Rustin M, Burrows NP, Bennett C, Harper JI, Conrad B, Verma IC, Taibjee SM, Moss C, O'Toole EA, Kelsell DP.

J Invest Dermatol. 2013 Feb;133(2):573-6. doi: 10.1038/jid.2012.332. Epub 2012 Sep 20. No abstract available.

PubMed [citation]

PMID:: 22992804

Genotype-phenotype correlation in a large English cohort of patients with autosomal recessive ichthyosis.

Simpson JK, Martinez-Queipo M, Onoufriadis A, Tso S, Glass E, Liu L, Higashino T, Scott W, Tierney C, Simpson MA, Desomchoke R, Youssefian L, SaeIdian AH, Vahidnezhad H, Bisquera A, Ravenscroft J, Moss C, O'Toole EA, Burrows N, Leech S, Jones EA, Lim D, et al.

Br J Dermatol. 2020 Mar;182(3):729-737. doi: 10.1111/bjd.18211. Epub 2019 Aug 26.

PubMed [citation]

PMID:: 31168818

See all PubMed Citations (5)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004389312.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (5)

Description

This variant is not present in population databases (gnomAD no frequency). For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. Disruption of this splice site has been observed in individuals with congenital ichythyosis (PMID: 22992804, 31168818; Invitae). This sequence change affects a donor splice site in intron 17 of the ABCA12 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in ABCA12 are known to be pathogenic (PMID: 20672373).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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