rs61751408

Positions:

• chr1-94005509-G-A

Variant summary

Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PM1 PP3 PP5_Very_Strong

The NM_000350.3(ABCA4):​c.6079C>T​(p.Leu2027Phe) variant causes a missense change. The variant allele was found at a frequency of 0.000469 in 1,614,112 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★).

• Frequency:
  • Genomes: 𝑓 0.00018 (0 hom., cov: 33)
  • Exomes 𝑓: 0.00050 (0 hom.)
• Consequence: ABCA4 NM_000350.3 missense
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:19 O:1
• Conservation: PhyloP100: 6.60

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 (HGNC:):

ACMG classification

Verdict is Pathogenic. Variant got 11 ACMG points.

• PM1: In a hotspot region, there are 6 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 5 uncertain in NM_000350.3
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.783
• PP5: Variant 1-94005509-G-A is Pathogenic according to our data. Variant chr1-94005509-G-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 7882.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-94005509-G-A is described in Lovd as [Likely_benign]. Variant chr1-94005509-G-A is described in Lovd as [Pathogenic]. Variant chr1-94005509-G-A is described in Lovd as [Likely_pathogenic]. Variant chr1-94005509-G-A is described in Lovd as [Likely_pathogenic]. Variant chr1-94005509-G-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ABCA4	NM_000350.3	c.6079C>T	p.Leu2027Phe	missense_variant	44/50	ENST00000370225.4	NP_000341.2
ABCA4	XM_047416704.1	c.5857C>T	p.Leu1953Phe	missense_variant	43/49

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ABCA4	ENST00000370225.4	c.6079C>T	p.Leu2027Phe	missense_variant	44/50	1	NM_000350.3	ENSP00000359245.3
ABCA4	ENST00000465352.1	n.495C>T		non_coding_transcript_exon_variant	5/6	5
ABCA4	ENST00000484388.1	n.193C>T		non_coding_transcript_exon_variant	2/2	2

Frequencies

GnomAD3 genomes AF: 0.000177 AC: 27 AN: 152166 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.000241

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000654

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000235

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.000199 AC: 50 AN: 251402 Hom.: 0 AF XY: 0.000221 AC XY: 30 AN XY: 135860

Gnomad AFR exome AF: 0.000185

Gnomad AMR exome AF: 0.0000578

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000387

Gnomad OTH exome AF: 0.000163

GnomAD4 exome AF: 0.000499 AC: 730 AN: 1461828 Hom.: 0 Cov.: 30 AF XY: 0.000491 AC XY: 357 AN XY: 727224

Gnomad4 AFR exome AF: 0.0000896

Gnomad4 AMR exome AF: 0.0000671

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000634

Gnomad4 OTH exome AF: 0.000315

GnomAD4 genome AF: 0.000177 AC: 27 AN: 152284 Hom.: 0 Cov.: 33 AF XY: 0.000134 AC XY: 10 AN XY: 74454

Gnomad4 AFR AF: 0.000241

Gnomad4 AMR AF: 0.0000654

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000235

Gnomad4 OTH AF: 0.00

Alfa AF: 0.000347 Hom.: 0

Bravo AF: 0.000223

TwinsUK AF: 0.000809 AC: 3

ALSPAC AF: 0.00 AC: 0

ESP6500AA AF: 0.000227 AC: 1

ESP6500EA AF: 0.000349 AC: 3

ExAC AF: 0.000214 AC: 26

EpiCase AF: 0.000382

EpiControl AF: 0.000296

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:19 Other:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Pathogenic:6 Other:1

Pathogenic, no assertion criteria provided	clinical testing	Department of Pathology and Laboratory Medicine, Sinai Health System	-	The ABCA4 p.Leu2027Phe variant was identified in 44 of 428 proband chromosomes (frequency: 0.103) from individuals or families with Stargardt Disease, Cone-Rod dystrophy or ABCA4-Associated Retinopathies (Maugeri_1999_PMID:10090887; Bertelsen_2014_PMID:24713488; Heathfield_2013_PMID:23695285, Fishman_2003_PMID:12796258). The variant was identified in dbSNP (ID: rs61751408) and in ClinVar (classified as pathogenic by EGL Genetic Diagnostics, Fulgent Genetics, GeneDx and Institute of Human Genetics, Univ. Regensburg). The variant was also identified in control databases in 56 of 282804 chromosomes at a frequency of 0.000198 (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: European (non-Finnish) in 45 of 129122 chromosomes (freq: 0.000349), African in 8 of 24968 chromosomes (freq: 0.00032), Other in 1 of 7222 chromosomes (freq: 0.000139) and Latino in 2 of 35436 chromosomes (freq: 0.000056); it was not observed in the Ashkenazi Jewish, East Asian, European (Finnish) and South Asian populations. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a difference in splicing. The p.Leu2027 residue is conserved in mammals and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) provide inconsistent predictions regarding the impact to the protein. However, in vitro functional studies of the L2027F variant have demonstrated biochemical defects leading to lower protein functionality and altered ATPase function (Sun_2000_PMID: 11017087; Biswas_2000_PMID: 11123914). In summary, based on the above information this variant meets our laboratory’s criteria to be classified as pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Jun 18, 2018	- -
Pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Nov 01, 2016	- -
not provided, no classification provided	literature only	Retina International	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 29, 2024	This sequence change replaces leucine, which is neutral and non-polar, with phenylalanine, which is neutral and non-polar, at codon 2027 of the ABCA4 protein (p.Leu2027Phe). This variant is present in population databases (rs61751408, gnomAD 0.03%). This missense change has been observed in individuals with Stargardt disease (PMID: 28559085). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 7882). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt ABCA4 protein function with a positive predictive value of 95%. Experimental studies have shown that this missense change affects ABCA4 function (PMID: 29847635). For these reasons, this variant has been classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Sep 29, 2022	Published functional studies demonstrate a damaging effect with decreased ATPase function of the protein, reduced expression compared to wild-type, and abnormal localization to the endoplasmic reticulum (Biswas et al., 2000; Garces et al., 2018); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 9666097, 11527935, 11702214, 29884405, 29701254, 29310964, 31429209, 32531858, 33706644, 34795310, 34946930, 35456422, 23695285, 19074458, 24713488, 14517951, 9973280, 11328725, 11726554, 10396622, 10090887, 15161829, 29555955, 29847635, 30609409, 30093795, 30060493, 29126757, 30563929, 27820952, 28559085, 32845050, 9054934, 31589614, 32810830, 33546218, 11123914, 29925512) -
Pathogenic, criteria provided, single submitter	clinical testing	Knight Diagnostic Laboratories, Oregon Health and Sciences University	May 11, 2018	- -

Severe early-childhood-onset retinal dystrophy Pathogenic:6

Pathogenic, no assertion criteria provided	literature only	OMIM	Jun 01, 2003	- -
Pathogenic, criteria provided, single submitter	clinical testing	Molecular Genetics, Royal Melbourne Hospital	Mar 30, 2023	This sequence change is predicted to replace leucine with phenylalanine at codon 2027 of the ABCA4 protein (p.Leu2027Phe). The leucine residue is highly conserved (100 vertebrates, UCSC), and located in the cytoplasmic ATP-binding cassette (ABC) transporter 2 domain. There is a small physicochemical difference between leucine and phenylalanine. The variant is present in a large population cohort at a frequency of 0.02%, which is consistent with recessive carrier frequency (rs61751408, 56/282,804 alleles, 0 homozygotes in gnomAD v2.1.1 - PM2). It is a recurrent variant that has been identified as compound heterozygous or homozygous in multiple Stargardt disease patients, with homozygous cases demonstrating a milder phenotype (PMID: 9054934, 23695285, 23769331 - PM3_VeryStrong). The missense change significantly reduces the ATPase function of the ABC transporter domain in multiple in vitro functional assays (PMID: 11017087, 11123914 - PS3). Multiple lines of computational evidence predict a deleterious effect for the missense substitution (7/7 algorithms - PP3). Based on the classification scheme RMH ACMG Guidelines v1.1.1, this variant is classified as PATHOGENIC. Following criteria are met: PM3_VeryStrong, PS3, PM2, PP3. -
Pathogenic, criteria provided, single submitter	clinical testing	Institute of Human Genetics, University of Leipzig Medical Center	Jan 17, 2020	Criteria applied: PS3,PM3_STR,PP3 -
Pathogenic, criteria provided, single submitter	clinical testing	Victorian Clinical Genetics Services, Murdoch Childrens Research Institute	Jun 24, 2022	Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with Stargardt disease 1 (MIM#248200). (I) 0106 - This gene is associated with autosomal recessive disease. (I) 0115 - Variants in this gene are known to have variable expressivity (PMID: 31522899). (I) 0200 - Variant is predicted to result in a missense amino acid change from leucine to phenylalanine. (I) 0251 - This variant is heterozygous. (I) 0304 - Variant is present in gnomAD <0.01 (v2 & v3) for a recessive condition (74 heterozygotes, 0 homozygotes). (SP) 0502 - Missense variant with conflicting in silico predictions and uninformative conservation. (I) 0600 - Variant is located in the annotated ABC transporter domain (DECIPHER). (I) 0801 - This variant has very strong previous evidence of pathogenicity in unrelated individuals. It has been reported in multiple individuals with autosomal recessive Stargardt disease (ClinVar, PMID: 23695285). (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign -
Pathogenic, criteria provided, single submitter	clinical testing	Institute of Human Genetics, Univ. Regensburg, Univ. Regensburg	Jan 01, 2016	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Institute of Medical Molecular Genetics, University of Zurich	Jan 30, 2021	- -

Cone-rod dystrophy 3 Pathogenic:2

Pathogenic, no assertion criteria provided	literature only	OMIM	Jun 01, 2003	- -
Pathogenic, criteria provided, single submitter	clinical testing	Institute of Human Genetics, University of Leipzig Medical Center	Jan 01, 2019	- -

Retinal dystrophy Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Blueprint Genetics	Aug 12, 2019	- -
Pathogenic, criteria provided, single submitter	clinical testing	Institute of Human Genetics, Univ. Regensburg, Univ. Regensburg	Jan 01, 2023	- -

Age related macular degeneration 2 Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Mendelics

May 04, 2022

- -

Severe early-childhood-onset retinal dystrophy;C1858806:Cone-rod dystrophy 3;C1866422:Retinitis pigmentosa 19;C3495438:Age related macular degeneration 2 Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

Oct 31, 2018

- -

Stargardt disease Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Nov 10, 2016

The p.Leu2027Phe variant in ABCA4 has been reported in over 30 individuals with Stargardt disease, including 28 compound heterozygous and 3 homozygous individua ls (Allikmets 1997, Bertelsen 2014, Heathfield 2013, Fujinami 2013). Of note, t he individuals homozygous for this variant presented with a later onset and mild er phenotype (Fujinami 2013, Heathfield 2013). The variant has been identified i n 23/66736 of European chromosomes by the Exome Aggregation Consortium (ExAC, ht tp://exac.broadinstitute.org; dbSNP rs61751408). Although this variant has been seen in the general population, its frequency is low enough to be consistent wit h a recessive carrier frequency. In vitro functional studies provide some evide nce that the p.Leu2027Phe variant may impact protein function (Biswas 2000). In summary, this variant meets criteria to be classified as pathogenic for Stargard t disease in an autosomal recessive manner based upon observation in patients wi th this disease and functional evidence. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.61
BayesDel_addAF	Pathogenic	0.25	D
BayesDel_noAF	Pathogenic	0.48
CADD	Pathogenic	28
DANN	Pathogenic	1.0
DEOGEN2	Pathogenic	0.80	D;D
Eigen	Pathogenic	0.86
Eigen_PC	Pathogenic	0.86
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Uncertain	0.97	D;D
M_CAP	Uncertain	0.12	D
MetaRNN	Pathogenic	0.78	D;D
MetaSVM	Pathogenic	1.1	D
MutationAssessor	Benign	1.2	.;L
PrimateAI	Uncertain	0.65	T
PROVEAN	Uncertain	-3.7	.;D
REVEL	Pathogenic	0.95
Sift	Uncertain	0.0020	.;D
Sift4G	Uncertain	0.0020	D;D
Polyphen		1.0	.;D
Vest4		0.98
MVP		0.98
MPC		0.48
ClinPred		0.29	T
GERP RS		5.9
Varity_R		0.80
gMVP		0.91

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

LitVar

Other links and lift over

dbSNP: rs61751408; hg19: chr1-94471065;