1-68438228-G-T

Variant summary

Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PM1PM2PM5PP3_ModeratePP5_Very_Strong

The NM_000329.3(RPE65):c.1087C>A(p.Pro363Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000684 in 1,461,686 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 Pathogenic (★★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P363H) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)

Exomes 𝑓: 0.0000068 ( 0 hom. )

Consequence

RPE65
NM_000329.3 missense

Scores

Clinical Significance

Pathogenic reviewed by expert panel P:7

Conservation

PhyloP100: 9.48

Variant links:

Genes affected

RPE65 (HGNC:10294): (retinoid isomerohydrolase RPE65) The protein encoded by this gene is a component of the vitamin A visual cycle of the retina which supplies the 11-cis retinal chromophore of the photoreceptors opsin visual pigments. It is a member of the carotenoid cleavage oxygenase superfamily. All members of this superfamily are non-heme iron oxygenases with a seven-bladed propeller fold and oxidatively cleave carotenoid carbon:carbon double bonds. However, the protein encoded by this gene has acquired a divergent function that involves the concerted O-alkyl ester cleavage of its all-trans retinyl ester substrate and all-trans to 11-cis double bond isomerization of the retinyl moiety. As such, it performs the essential enzymatic isomerization step in the synthesis of 11-cis retinal. Mutations in this gene are associated with early-onset severe blinding disorders such as Leber congenital. [provided by RefSeq, Oct 2017]

RPE65 links:

LOC124904198 (HGNC:):

LOC124904198 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 16 ACMG points.

PM1

In a hotspot region, there are 2 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 4 uncertain in NM_000329.3

PM2

Very rare variant in population databases, with high coverage;

PM5

Other missense variant is known to change same aminoacid residue: Variant chr1-68438228-G-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 1803135.Status of the report is criteria_provided_single_submitter, 1 stars.

PP3

MetaRNN computational evidence supports a deleterious effect, 0.919

PP5

Variant 1-68438228-G-T is Pathogenic according to our data. Variant chr1-68438228-G-T is described in ClinVar as [Pathogenic]. Clinvar id is 13117.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr1-68438228-G-T is described in Lovd as [Pathogenic]. Variant chr1-68438228-G-T is described in Lovd as [Likely_pathogenic]. Variant chr1-68438228-G-T is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RPE65	NM_000329.3 linkuse as main transcript	c.1087C>A	p.Pro363Thr	missense_variant	10/14	ENST00000262340.6
LOC124904198	XR_007066164.1 linkuse as main transcript	n.72-10304G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RPE65	ENST00000262340.6 linkuse as main transcript	c.1087C>A	p.Pro363Thr	missense_variant	10/14	1	NM_000329.3	P1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD3 exomes

AF:

0.0000159

AC:

AN:

251282

Hom.:

AF XY:

0.0000221

AC XY:

AN XY:

135816

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000131

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.00000684

AC:

AN:

1461686

Hom.:

Cov.:

AF XY:

0.0000110

AC XY:

AN XY:

727146

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000104

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00

Gnomad4 OTH exome

AF:

0.0000166

GnomAD4 genome

Cov.:

ExAC

AF:

0.0000165

AC:

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:7

Revision: reviewed by expert panel

LINK: link

Submissions by phenotype

Leber congenital amaurosis 2

Pathogenic:3

Pathogenic, criteria provided, single submitter	clinical testing	MGZ Medical Genetics Center	Mar 28, 2022	- -
Pathogenic, no assertion criteria provided	research	Laboratory of Genetics in Ophthalmology, Institut Imagine	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Oct 19, 2023	- -

RPE65-related recessive retinopathy

Pathogenic:1

Pathogenic, reviewed by expert panel

curation

ClinGen Leber Congenital Amaurosis/early Onset Retinal Dystrophy Variant Curation Expert Panel, ClinGen

Dec 22, 2023

The NM_000329.3(RPE65):c.1087C>A (p.Pro363Thr) variant is reported in the literature in a homozygous state in at least two probands affected with Leber congenital amaurosis or early onset severe retinal dystrophy (1 point, PM3, PMID: 9326941, PMID: 26352687). At least one patient harboring the variant exhibited reduced or nondetectable rod ERG (required, 0.5 pts), decreased central visual acuity (1 pt), symptomatic onset between birth and age 5 years (1 pt), evidence of cone involvement on ERG (1 pt), light staring (1 pt), nyctalopia (0.5 pts), and positive response to RPE65 gene therapy (8 pts), which together are specific for RPE65-related recessive retinopathy (13 pts total, VCEP member-provided data, PP4_Moderate). The variant has been reported to segregate with childhood-onset severe retinal dystrophy in multiple families with at least 3 members (PP1_strong, PMID:9326941, PMID: 26352687). This variant is reported in ClinVar (Variation ID: 13117), and its Popmax Filtering AF in gnomAD v.2.1.1 is 0.00004443 (4/30608 alleles) in the South Asian population, which is lower than the ClinGen LCA / eoRD VCEP threshold (<0.0002) (PM2_Supporting). The meta-predictor REVEL gives a score of 0.702, which is above the ClinGen LCA/eoRD VCEP PP3 threshold of >0.644 and predicts a damaging effect on RPE65 function (PP3). An in vitro isomerohydrolase activity assay performed in adenovirus-infected 293A-LRAT cells showed that the p.Pro363Thr mutant exhibits complete loss of 11-cis-retinol production relative to the wild-type RPE65 control, confirming that this variant has a damaging effect on protein function (PMID: 16828753, PS3_supporting). In summary, this variant meets the criteria to be classified as Pathogenic for RPE65-related recessive retinopathy based on the ACMG/AMP criteria applied, as specified by the ClinGen LCA/eoRD VCEP: PP1_Strong, PM3, PP4_Moderate, PS3_Supporting, PM2_Supporting, PP3. (VCEP specifications version 1.0.0; date of approval 09/21/2023). -

Leber congenital amaurosis 2;C3151086:Retinitis pigmentosa 20

Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Invitae

May 17, 2022

This sequence change replaces proline, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 363 of the RPE65 protein (p.Pro363Thr). This variant is present in population databases (rs121917744, gnomAD 0.01%). This missense change has been observed in individuals with Leber congenital amaurosis and retinal dystrophy (PMID: 9326941, 15024725, 29332120). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 13117). 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 RPE65 protein function. Experimental studies have shown that this missense change affects RPE65 function (PMID: 16828753). For these reasons, this variant has been classified as Pathogenic. -

Leber congenital amaurosis

Pathogenic:1

Pathogenic, no assertion criteria provided

clinical testing

Natera, Inc.

Nov 09, 2020

- -

Retinitis pigmentosa 20

Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Oct 01, 1997

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.93

BayesDel_addAF

Pathogenic

0.31

BayesDel_noAF

Pathogenic

0.44

Cadd

Benign

Dann

Uncertain

1.0

DEOGEN2

Pathogenic

0.80

Eigen

Uncertain

0.53

Eigen_PC

Uncertain

0.61

FATHMM_MKL

Pathogenic

0.99

LIST_S2

Uncertain

0.96

M_CAP

Uncertain

0.16

MetaRNN

Pathogenic

0.92

MetaSVM

Uncertain

0.54

MutationAssessor

Uncertain

2.4

MutationTaster

Benign

1.0

PrimateAI

Uncertain

0.55

PROVEAN

Benign

-1.7

REVEL

Pathogenic

0.70

Sift

Benign

0.063

Sift4G

Benign

0.63

Polyphen

0.64

Vest4

0.96

MutPred

0.75

Gain of MoRF binding (P = 0.0359);

MVP

0.99

MPC

0.34

ClinPred

0.58

GERP RS

5.7

Varity_R

0.17

gMVP

0.86

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.060

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over