NM_000329.3:c.394G>A

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BS3_SupportingBA1

This summary comes from the ClinGen Evidence Repository: NM_000329.3(RPE65):c.394G>A is a missense variant that replaces alanine with threonine at codon 132. This variant is present in gnomAD v.2.1.1 at a GrpMax allele frequency of 0.01113, with 372 alleles / 30614 total alleles in the South Asian population (with 6 homozygotes), which is higher than the ClinGen LCA / eoRD VCEP BA1 threshold of >0.008 (BA1). The computational predictor REVEL gives a score of 0.548, which is above the ClinGen LCA / eoRD VCEP threshold of <0.3 and does not strongly predict a non-damaging effect on RPE65 function. The splicing impact predictor SpliceAI gives a score of 0.03 for splice acceptor loss, which is below the ClinGen LCA / eoRD VCEP recommended threshold of ≥0.2 and does not strongly predict an impact on splicing. The variant exhibited 50% enzymatic activity in an isomerohydrolase assay relative to the wild-type control, which is higher than the ClinGen LCA / eoRD BS3_Supporting threshold of >50% activity, indicating that it largely preserves] normal protein function (PMID:16150724, BS3_Supporting). In summary, this variant meets the criteria to be classified as benign for RPE65-related recessive retinopathy based on the ACMG/AMP criteria applied, as specified by the ClinGen LCA/eoRD VCEP: BA1, BS3_Supporting. (VCEP specifications version 1.0.0; date of approval 09/21/2023). LINK:https://erepo.genome.network/evrepo/ui/classification/CA226547/MONDO:0100368/120

Frequency

Genomes: 𝑓 0.0015 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0017 ( 26 hom. )

Consequence

RPE65
NM_000329.3 missense

Scores

1
7
10

Clinical Significance

Benign reviewed by expert panel U:2B:11O:1

Conservation

PhyloP100: 5.74
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BS3
For more information check the summary or visit ClinGen Evidence Repository.
BA1
For more information check the summary or visit ClinGen Evidence Repository.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
RPE65NM_000329.3 linkc.394G>A p.Ala132Thr missense_variant Exon 5 of 14 ENST00000262340.6 NP_000320.1 Q16518

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
RPE65ENST00000262340.6 linkc.394G>A p.Ala132Thr missense_variant Exon 5 of 14 1 NM_000329.3 ENSP00000262340.5 Q16518

Frequencies

GnomAD3 genomes
AF:
0.00147
AC:
224
AN:
152118
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0000966
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000720
Gnomad ASJ
AF:
0.0193
Gnomad EAS
AF:
0.000386
Gnomad SAS
AF:
0.0139
Gnomad FIN
AF:
0.0000943
Gnomad MID
AF:
0.00637
Gnomad NFE
AF:
0.00101
Gnomad OTH
AF:
0.000478
GnomAD3 exomes
AF:
0.00294
AC:
739
AN:
251320
Hom.:
9
AF XY:
0.00352
AC XY:
478
AN XY:
135880
show subpopulations
Gnomad AFR exome
AF:
0.000185
Gnomad AMR exome
AF:
0.000954
Gnomad ASJ exome
AF:
0.0211
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0122
Gnomad FIN exome
AF:
0.0000462
Gnomad NFE exome
AF:
0.000836
Gnomad OTH exome
AF:
0.00359
GnomAD4 exome
AF:
0.00168
AC:
2456
AN:
1461858
Hom.:
26
Cov.:
32
AF XY:
0.00200
AC XY:
1451
AN XY:
727232
show subpopulations
Gnomad4 AFR exome
AF:
0.0000597
Gnomad4 AMR exome
AF:
0.000872
Gnomad4 ASJ exome
AF:
0.0208
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0116
Gnomad4 FIN exome
AF:
0.0000187
Gnomad4 NFE exome
AF:
0.000595
Gnomad4 OTH exome
AF:
0.00306
GnomAD4 genome
AF:
0.00145
AC:
221
AN:
152236
Hom.:
0
Cov.:
32
AF XY:
0.00150
AC XY:
112
AN XY:
74446
show subpopulations
Gnomad4 AFR
AF:
0.0000963
Gnomad4 AMR
AF:
0.000719
Gnomad4 ASJ
AF:
0.0193
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.0135
Gnomad4 FIN
AF:
0.0000943
Gnomad4 NFE
AF:
0.00101
Gnomad4 OTH
AF:
0.000473
Alfa
AF:
0.00171
Hom.:
1
Bravo
AF:
0.00112
TwinsUK
AF:
0.00108
AC:
4
ALSPAC
AF:
0.00104
AC:
4
ESP6500AA
AF:
0.000227
AC:
1
ESP6500EA
AF:
0.00163
AC:
14
ExAC
AF:
0.00287
AC:
348
Asia WGS
AF:
0.00318
AC:
11
AN:
3478
EpiCase
AF:
0.000927
EpiControl
AF:
0.00124

ClinVar

Significance: Benign
Submissions summary: Uncertain:2Benign:11Other:1
Revision: reviewed by expert panel
LINK: link

Submissions by phenotype

Leber congenital amaurosis 2 Benign:3
Aug 22, 2023
Mendelics
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Jun 10, 2021
Genome-Nilou Lab
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

-
Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: research

The p.Ala132Thr variant in RPE65 has been identified in 2 homozygous siblings from 1 family with retinitis pigmentosa (PMID: 9501220), and in the heterozygous state in 2 unrelated individuals with retinitis pigmentosa from India and Dubai respectively (PMID: 24066033, 24265693). In vitro functional studies provide some evidence that the p.Ala132Thr variant may slightly impact protein function (PMID: 16150724). However, these types of assays may not accurately represent biological function and this variant has been identified in >1% of South Asian chromosomes and 4 homozygotes by ExAC (http://gnomad.broadinstitute.org/). In summary, although additional studies are required to fully establish its clinical significance, this variant meets criteria to be classified as likely benign for autosomal recessive retinitis pigmentosa. -

not provided Benign:2Other:1
Feb 01, 2025
CeGaT Center for Human Genetics Tuebingen
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

RPE65: BS1, BS2 -

Feb 05, 2018
GeneDx
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

This variant is associated with the following publications: (PMID: 18722466, 21931134, 11095629, 16150724, 24066033, 9501220, 27535533, 26355662, 26626312) -

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

- -

Leber congenital amaurosis 2;C3151086:Retinitis pigmentosa 20 Benign:2
Mar 06, 2017
Counsyl
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Jan 30, 2025
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Leber congenital amaurosis Uncertain:1
Apr 03, 2020
Natera, Inc.
Significance: Uncertain significance
Review Status: no assertion criteria provided
Collection Method: clinical testing

- -

Retinitis pigmentosa 20 Uncertain:1
Mar 17, 1998
OMIM
Significance: Uncertain significance
Review Status: no assertion criteria provided
Collection Method: literature only

- -

not specified Benign:1
May 03, 2022
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

RPE65-related disorder Benign:1
Sep 10, 2024
PreventionGenetics, part of Exact Sciences
Significance: Benign
Review Status: no assertion criteria provided
Collection Method: clinical testing

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

RPE65-related recessive retinopathy Benign:1
Dec 22, 2023
ClinGen Leber Congenital Amaurosis/early Onset Retinal Dystrophy Variant Curation Expert Panel, ClinGen
Significance: Benign
Review Status: reviewed by expert panel
Collection Method: curation

NM_000329.3(RPE65):c.394G>A is a missense variant that replaces alanine with threonine at codon 132. This variant is present in gnomAD v.2.1.1 at a GrpMax allele frequency of 0.01113, with 372 alleles / 30614 total alleles in the South Asian population (with 6 homozygotes), which is higher than the ClinGen LCA / eoRD VCEP BA1 threshold of >0.008 (BA1). The computational predictor REVEL gives a score of 0.548, which is above the ClinGen LCA / eoRD VCEP threshold of <0.3 and does not strongly predict a non-damaging effect on RPE65 function. The splicing impact predictor SpliceAI gives a score of 0.03 for splice acceptor loss, which is below the ClinGen LCA / eoRD VCEP recommended threshold of greater than or equal to 0.2 and does not strongly predict an impact on splicing. The variant exhibited 50% enzymatic activity in an isomerohydrolase assay relative to the wild-type control, which is higher than the ClinGen LCA / eoRD BS3_Supporting threshold of >50% activity, indicating that it largely preserves] normal protein function (PMID: 16150724, BS3_Supporting). In summary, this variant meets the criteria to be classified as benign for RPE65-related recessive retinopathy based on the ACMG/AMP criteria applied, as specified by the ClinGen LCA/eoRD VCEP: BA1, BS3_Supporting. (VCEP specifications version 1.0.0; date of approval 09/21/2023). -

Retinal dystrophy Benign:1
Jan 01, 2022
Institute of Human Genetics, Univ. Regensburg, Univ. Regensburg
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.21
BayesDel_addAF
Uncertain
0.057
T
BayesDel_noAF
Pathogenic
0.32
CADD
Uncertain
23
DANN
Benign
0.97
DEOGEN2
Uncertain
0.76
D
Eigen
Benign
0.0099
Eigen_PC
Benign
0.20
FATHMM_MKL
Uncertain
0.94
D
LIST_S2
Uncertain
0.88
D
MetaRNN
Benign
0.014
T
MetaSVM
Uncertain
0.16
D
MutationAssessor
Benign
1.4
L
PrimateAI
Uncertain
0.61
T
PROVEAN
Benign
-0.76
N
REVEL
Uncertain
0.55
Sift
Benign
0.50
T
Sift4G
Benign
0.47
T
Polyphen
0.012
B
Vest4
0.78
MVP
0.96
MPC
0.054
ClinPred
0.019
T
GERP RS
5.0
Varity_R
0.23
gMVP
0.54

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.030
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.

Other links and lift over

dbSNP: rs61752878; hg19: chr1-68910315; API