rs796052338

Variant summary

Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong

The NM_001042432.2(CLN3):​c.1256G>A​(p.Gly419Glu) variant causes a missense change. The variant allele was found at a frequency of 0.00000372 in 1,613,768 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 Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: 𝑓 0.0000066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000034 ( 0 hom. )

Consequence

CLN3
NM_001042432.2 missense

Scores

13
5
1

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:2U:3

Conservation

PhyloP100: 6.69
Variant links:
Genes affected
CLN3 (HGNC:2074): (CLN3 lysosomal/endosomal transmembrane protein, battenin) This gene encodes a protein that is involved in lysosomal function. Mutations in this, as well as other neuronal ceroid-lipofuscinosis (CLN) genes, cause neurodegenerative diseases commonly known as Batten disease or collectively known as neuronal ceroid lipofuscinoses (NCLs). Many alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_pathogenic. Variant got 6 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.991

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CLN3NM_001042432.2 linkuse as main transcriptc.1256G>A p.Gly419Glu missense_variant 16/16 ENST00000636147.2 NP_001035897.1 Q13286-1A0A024QZB8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CLN3ENST00000636147.2 linkuse as main transcriptc.1256G>A p.Gly419Glu missense_variant 16/161 NM_001042432.2 ENSP00000490105.1 Q13286-1
ENSG00000261832ENST00000637378.1 linkuse as main transcriptc.228+4528G>A intron_variant 5 ENSP00000490831.1 A0A1B0GW90

Frequencies

GnomAD3 genomes
AF:
0.00000658
AC:
1
AN:
152032
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
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:
0.0000147
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.00000342
AC:
5
AN:
1461736
Hom.:
0
Cov.:
31
AF XY:
0.00000138
AC XY:
1
AN XY:
727156
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:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000450
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.00000658
AC:
1
AN:
152032
Hom.:
0
Cov.:
32
AF XY:
0.00
AC XY:
0
AN XY:
74266
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000147
Gnomad4 OTH
AF:
0.00
Bravo
AF:
0.00000756

ClinVar

Significance: Conflicting classifications of pathogenicity
Submissions summary: Pathogenic:2Uncertain:3
Revision: criteria provided, conflicting classifications
LINK: link

Submissions by phenotype

Neuronal ceroid lipofuscinosis 3 Uncertain:2
Uncertain significance, criteria provided, single submitterclinical testingCounsylApr 11, 2018- -
Uncertain significance, criteria provided, single submitterclinical testingGenome-Nilou LabSep 05, 2021- -
Neuronal ceroid lipofuscinosis Pathogenic:1
Pathogenic, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpDec 14, 2023This sequence change replaces glycine, which is neutral and non-polar, with glutamic acid, which is acidic and polar, at codon 419 of the CLN3 protein (p.Gly419Glu). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with an abnormality of the eye and/or clinical features of retinitis pigmentosa (PMID: 26633542; Invitae). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 205102). 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 CLN3 protein function with a positive predictive value of 80%. For these reasons, this variant has been classified as Pathogenic. -
early onset and severe retinal dystrophy Pathogenic:1
Likely pathogenic, no assertion criteria providedresearchLaboratory of Genetics in Ophthalmology, Institut Imagine-- -
not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingWomen's Health and Genetics/Laboratory Corporation of America, LabCorpApr 03, 2024Variant summary: CLN3 c.1256G>A (p.Gly419Glu) results in a non-conservative amino acid change in the encoded protein sequence. Four of four in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 250768 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.1256G>A has been reported in the literature in at-least one individual affected with Batten Disease (example, Griffith_2022, Retterer_2016). These data do not allow any conclusion about variant significance. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publications have been ascertained in the context of this evaluation (PMID: 36011402, 26633542). ClinVar contains an entry for this variant (Variation ID: 205102). Based on the evidence outlined above, the variant was classified as uncertain significance. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
1.0
BayesDel_addAF
Pathogenic
0.56
D
BayesDel_noAF
Pathogenic
0.57
CADD
Pathogenic
27
DANN
Uncertain
1.0
DEOGEN2
Pathogenic
0.98
D;D;.;.;D;.;.;D;D;D;.;D;.;.
Eigen
Pathogenic
0.76
Eigen_PC
Uncertain
0.65
FATHMM_MKL
Uncertain
0.95
D
LIST_S2
Uncertain
0.95
.;.;D;.;.;D;D;D;.;D;D;D;.;D
M_CAP
Pathogenic
0.79
D
MetaRNN
Pathogenic
0.99
D;D;D;D;D;D;D;D;D;D;D;D;D;D
MetaSVM
Pathogenic
1.1
D
MutationAssessor
Pathogenic
4.0
H;H;.;.;.;.;.;.;H;.;.;.;.;.
PrimateAI
Uncertain
0.69
T
PROVEAN
Pathogenic
-7.3
.;D;.;.;D;D;D;N;D;.;D;.;.;D
REVEL
Pathogenic
0.95
Sift
Pathogenic
0.0
.;D;.;.;D;D;D;T;D;.;D;.;.;D
Sift4G
Pathogenic
0.0
.;.;D;.;D;D;D;.;D;.;D;.;.;.
Polyphen
1.0
D;D;.;.;D;.;.;.;D;D;D;D;.;D
Vest4
0.82, 0.93, 0.94, 0.93, 0.94, 0.95
MutPred
0.95
Gain of glycosylation at S423 (P = 0.1323);Gain of glycosylation at S423 (P = 0.1323);.;.;.;.;.;.;Gain of glycosylation at S423 (P = 0.1323);.;.;.;.;.;
MVP
0.96
MPC
0.72
ClinPred
1.0
D
GERP RS
4.2
Varity_R
0.96
gMVP
0.98

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

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

Other links and lift over

dbSNP: rs796052338; hg19: chr16-28488898; COSMIC: COSV61107378; COSMIC: COSV61107378; API