GeneBe

rs281865386

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_000350.3(ABCA4):​c.1356+10delG variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as not provided (no stars).

Frequency

Genomes: not found (cov: 0)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

ABCA4
NM_000350.3 intron

Scores

Not classified

Clinical Significance

not provided no classification provided O:1

Conservation

PhyloP100: -1.16

Publications

2 publications found
Variant links:
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]
ABCA4 Gene-Disease associations (from GenCC):
  • ABCA4-related retinopathy
    Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
  • cone-rod dystrophy 3
    Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P, Ambry Genetics
  • severe early-childhood-onset retinal dystrophy
    Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Laboratory for Molecular Medicine, Labcorp Genetics (formerly Invitae), Ambry Genetics
  • retinitis pigmentosa 19
    Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
  • cone-rod dystrophy
    Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
  • retinitis pigmentosa
    Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
  • Stargardt disease
    Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ABCA4NM_000350.3 linkc.1356+10delG intron_variant Intron 10 of 49 ENST00000370225.4 NP_000341.2
ABCA4NM_001425324.1 linkc.1356+10delG intron_variant Intron 10 of 48 NP_001412253.1
LOC124904222XR_007066231.1 linkn.203-5144delC intron_variant Intron 1 of 1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ABCA4ENST00000370225.4 linkc.1356+10delG intron_variant Intron 10 of 49 1 NM_000350.3 ENSP00000359245.3
ABCA4ENST00000649773.1 linkc.1356+10delG intron_variant Intron 10 of 18 ENSP00000496882.1

Frequencies

GnomAD3 genomes
Cov.:
0
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
986690
Hom.:
0
Cov.:
22
AF XY:
0.00
AC XY:
0
AN XY:
509518
African (AFR)
AF:
0.00
AC:
0
AN:
25378
American (AMR)
AF:
0.00
AC:
0
AN:
42920
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
22338
East Asian (EAS)
AF:
0.00
AC:
0
AN:
35244
South Asian (SAS)
AF:
0.00
AC:
0
AN:
77206
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
50356
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
4770
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
684754
Other (OTH)
AF:
0.00
AC:
0
AN:
43724
GnomAD4 genome
Cov.:
0

ClinVar

Significance: not provided
Submissions summary: Other:1
Revision: no classification provided
LINK: link

Submissions by phenotype

not provided Other:1
Retina International
Significance:not provided
Review Status:no classification provided
Collection Method:literature only

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
-1.2

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

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

Publications

Other links and lift over

dbSNP: rs281865386; hg19: chr1-94544135; API