rs796052338
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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
NM_001042432.2 missense
Scores
13
5
1
Clinical Significance
Conservation
PhyloP100: 6.69
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]
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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 |
---|---|---|---|---|---|---|---|---|
CLN3 | NM_001042432.2 | c.1256G>A | p.Gly419Glu | missense_variant | 16/16 | ENST00000636147.2 | NP_001035897.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CLN3 | ENST00000636147.2 | c.1256G>A | p.Gly419Glu | missense_variant | 16/16 | 1 | NM_001042432.2 | ENSP00000490105.1 | ||
ENSG00000261832 | ENST00000637378.1 | c.228+4528G>A | intron_variant | 5 | ENSP00000490831.1 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152032Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461736Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727156
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GnomAD4 genome AF: 0.00000658 AC: 1AN: 152032Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74266
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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 submitter | clinical testing | Counsyl | Apr 11, 2018 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Sep 05, 2021 | - - |
Neuronal ceroid lipofuscinosis Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 14, 2023 | This 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 provided | research | Laboratory of Genetics in Ophthalmology, Institut Imagine | - | - - |
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Apr 03, 2024 | Variant 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:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Pathogenic
D;D;.;.;D;.;.;D;D;D;.;D;.;.
Eigen
Pathogenic
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
.;.;D;.;.;D;D;D;.;D;D;D;.;D
M_CAP
Pathogenic
D
MetaRNN
Pathogenic
D;D;D;D;D;D;D;D;D;D;D;D;D;D
MetaSVM
Pathogenic
D
MutationAssessor
Pathogenic
H;H;.;.;.;.;.;.;H;.;.;.;.;.
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
.;D;.;.;D;D;D;N;D;.;D;.;.;D
REVEL
Pathogenic
Sift
Pathogenic
.;D;.;.;D;D;D;T;D;.;D;.;.;D
Sift4G
Pathogenic
.;.;D;.;D;D;D;.;D;.;D;.;.;.
Polyphen
D;D;.;.;D;.;.;.;D;D;D;D;.;D
Vest4
0.82, 0.93, 0.94, 0.93, 0.94, 0.95
MutPred
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
D
GERP RS
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gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at