rs1553196583

Variant names:

• chr1-94111452-GT-G
• rs1553196583
• NM_000350.3:c.287delA

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1 PM2 PP5_Very_Strong

The NM_000350.3(ABCA4):​c.287delA​(p.Asn96ThrfsTer19) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★★). Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 33)
• Consequence: ABCA4 NM_000350.3 frameshift
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:2
• Conservation: PhyloP100: 7.88

Genes affected

ABCA4 (HGNC:34): (ATP binding cassette subfamily A member 4) The membrane-associated protein encoded by this gene is a member of the superfamily of ATP-binding cassette (ABC) transporters. ABC proteins transport various molecules across extra- and intracellular membranes. ABC genes are divided into seven distinct subfamilies (ABC1, MDR/TAP, MRP, ALD, OABP, GCN20, White). This protein is a member of the ABC1 subfamily. Members of the ABC1 subfamily comprise the only major ABC subfamily found exclusively in multicellular eukaryotes. This protein is a retina-specific ABC transporter with N-retinylidene-PE as a substrate. It is expressed exclusively in retina photoreceptor cells, and the gene product mediates transport of an essental molecule, all-trans-retinal aldehyde (atRAL), across the photoreceptor cell membrane. Mutations in this gene are found in patients diagnosed with Stargardt disease, a form of juvenile-onset macular degeneration. Mutations in this gene are also associated with retinitis pigmentosa-19, cone-rod dystrophy type 3, early-onset severe retinal dystrophy, fundus flavimaculatus, and macular degeneration age-related 2. [provided by RefSeq, Sep 2019]

ACMG classification

Verdict is Pathogenic. Variant got 18 ACMG points.

• PVS1: Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 1-94111452-GT-G is Pathogenic according to our data. Variant chr1-94111452-GT-G is described in ClinVar as [Pathogenic]. Clinvar id is 545516.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-94111452-GT-G is described in Lovd as [Pathogenic]. Variant chr1-94111452-GT-G is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ABCA4	NM_000350.3	c.287delA	p.Asn96ThrfsTer19	frameshift_variant	Exon 3 of 50	ENST00000370225.4	NP_000341.2
ABCA4	NM_001425324.1	c.287delA	p.Asn96ThrfsTer19	frameshift_variant	Exon 3 of 49		NP_001412253.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABCA4	ENST00000370225.4	c.287delA	p.Asn96ThrfsTer19	frameshift_variant	Exon 3 of 50	1	NM_000350.3	ENSP00000359245.3
ABCA4	ENST00000649773.1	c.287delA	p.Asn96ThrfsTer19	frameshift_variant	Exon 3 of 19			ENSP00000496882.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 34

GnomAD4 genome Cov.: 33

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Severe early-childhood-onset retinal dystrophy Pathogenic:1

Mar 05, 2018

Servicio Extremeño de Salud, Hospital de Mérida

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Found in two patients from the same family with Stargardt disease. This mutation was in trans with two other known mutations causing Stargardt dissease, rs41292677 and rs281865377, that were in the same allele. -

not provided Pathogenic:1

Jul 28, 2021

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

For these reasons, this variant has been classified as Pathogenic. This sequence change creates a premature translational stop signal (p.Asn96Thrfs*19) in the ABCA4 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in ABCA4 are known to be pathogenic (PMID: 10958761, 24938718, 25312043, 26780318). This variant is not present in population databases (ExAC no frequency). This premature translational stop signal has been observed in individual(s) with inherited retinal dystrophy (PMID: 23940504). ClinVar contains an entry for this variant (Variation ID: 545516). -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1553196583; hg19: chr1-94577008;