NM_173076.3(ABCA12):c.7444C>T (p.Arg2482Ter) AND Autosomal recessive congenital ichthyosis 4B

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Nov 15, 2022
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000677681.3

Allele description [Variation Report for NM_173076.3(ABCA12):c.7444C>T (p.Arg2482Ter)]

NM_173076.3(ABCA12):c.7444C>T (p.Arg2482Ter)

Genes:

ABCA12:ATP binding cassette subfamily A member 12 [Gene - OMIM - HGNC]
SNHG31:small nucleolar RNA host gene 31 [Gene - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2q35

Genomic location:

Preferred name:

NM_173076.3(ABCA12):c.7444C>T (p.Arg2482Ter)

Other names:

p.Arg2482Ter

HGVS:

NC_000002.12:g.214937608G>A
NG_007074.1:g.205820C>T
NM_015657.4:c.6490C>T
NM_173076.3:c.7444C>TMANE SELECT
NP_056472.2:p.Arg2164Ter
NP_056472.2:p.Arg2164Ter
NP_775099.2:p.Arg2482Ter
NC_000002.11:g.215802332G>A
NM_015657.3:c.6490C>T
NM_173076.2:c.7444C>T
NR_103740.2:n.7942C>T

Protein change:

R2164*

Links:

dbSNP: rs199503269

NCBI 1000 Genomes Browser:

rs199503269

Molecular consequence:

NR_103740.2:n.7942C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_015657.4:c.6490C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_173076.3:c.7444C>T - nonsense - [Sequence Ontology: SO:0001587]

Functional consequence:

unknown functional consequence

Observations:

Condition(s)

Name:: Autosomal recessive congenital ichthyosis 4B (ARCI4B)
Synonyms:: Harlequin ichthyosis; Ichthyosis congenita, Harlequin fetus type; Harlequin Fetus; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0009443; MedGen: C0598226; Orphanet: 457; OMIM: 242500

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000803824	Equipe Genetique des Anomalies du Developpement, Université de Bourgogne - Clinvar_gadteam_Clinical_exome_analysis_3	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Aug 5, 2016)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002764607	Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Nov 15, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000803824

Equipe Genetique des Anomalies du Developpement, Université de Bourgogne - Clinvar_gadteam_Clinical_exome_analysis_3

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Aug 5, 2016)

unknown

clinical testing

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

SCV002764607

Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Nov 15, 2022)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	1	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	yes	not provided	not provided	not provided	not provided	not provided	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

Details of each submission

From Equipe Genetique des Anomalies du Developpement, Université de Bourgogne - Clinvar_gadteam_Clinical_exome_analysis_3, SCV000803824.1

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

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

From Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics, SCV002764607.1

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

Description

A homozygous nonsense variation in exon 51 of the ABCA12 gene that results in a stop codon and premature truncation of the protein at codon 2482 was detected. The observed variation has previously been reported in patients with Herlequin ichthyosis (PMID:17684380). The variant has a minor allele frequency of 0.02% in the 1000 genomes database. The reference region is conserved across species. In summary, the variant meets our criteria to be classified as pathogenic.

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

Last Updated: Sep 29, 2024

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