rs104894483

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong

The ENST00000249806.11(CLN6):​c.214G>T​(p.Glu72Ter) variant causes a stop gained change. The variant allele was found at a frequency of 0.0000353 in 1,613,614 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 (★★). Synonymous variant affecting the same amino acid position (i.e. E72E) has been classified as Likely benign. Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: 𝑓 0.00023 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000015 ( 0 hom. )

Consequence

CLN6
ENST00000249806.11 stop_gained

Scores

4
2
1

Clinical Significance

Pathogenic criteria provided, multiple submitters, no conflicts P:6O:1

Conservation

PhyloP100: 3.88
Variant links:
Genes affected
CLN6 (HGNC:2077): (CLN6 transmembrane ER protein) This gene is one of eight which have been associated with neuronal ceroid lipofuscinoses (NCL). Also referred to as Batten disease, NCL comprises a class of autosomal recessive, neurodegenerative disorders affecting children. The genes responsible likely encode proteins involved in the degradation of post-translationally modified proteins in lysosomes. The primary defect in NCL disorders is thought to be associated with lysosomal storage function. [provided by RefSeq, Oct 2008]

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ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 18 ACMG points.

PVS1
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 15-68214373-C-A is Pathogenic according to our data. Variant chr15-68214373-C-A is described in ClinVar as [Pathogenic]. Clinvar id is 4077.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CLN6NM_017882.3 linkuse as main transcriptc.214G>T p.Glu72Ter stop_gained 3/7 ENST00000249806.11 NP_060352.1
CLN6NM_001411068.1 linkuse as main transcriptc.310G>T p.Glu104Ter stop_gained 3/7 NP_001397997.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CLN6ENST00000249806.11 linkuse as main transcriptc.214G>T p.Glu72Ter stop_gained 3/71 NM_017882.3 ENSP00000249806 P1Q9NWW5-1

Frequencies

GnomAD3 genomes
AF:
0.000230
AC:
35
AN:
152218
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00229
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:
0.00
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000676
AC:
17
AN:
251428
Hom.:
0
AF XY:
0.0000589
AC XY:
8
AN XY:
135902
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.000463
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:
0.00000879
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000151
AC:
22
AN:
1461396
Hom.:
0
Cov.:
30
AF XY:
0.0000124
AC XY:
9
AN XY:
727032
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.000380
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:
0.00000360
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.000230
AC:
35
AN:
152218
Hom.:
0
Cov.:
33
AF XY:
0.000403
AC XY:
30
AN XY:
74362
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00229
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00
Bravo
AF:
0.000238
ExAC
AF:
0.0000165
AC:
2
EpiCase
AF:
0.00
EpiControl
AF:
0.0000593

ClinVar

Significance: Pathogenic
Submissions summary: Pathogenic:6Other:1
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

Ceroid lipofuscinosis, neuronal, 6A Pathogenic:2Other:1
Pathogenic, no assertion criteria providedliterature onlyOMIMFeb 01, 2002- -
not provided, no classification providedliterature onlyGeneReviews-- -
Pathogenic, criteria provided, single submitterclinical testingCounsylMar 12, 2018- -
not provided Pathogenic:2
Pathogenic, criteria provided, single submitterclinical testingGeneDxMay 03, 2022Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; This variant is associated with the following publications: (PMID: 16857350, 12815591, 11791207, 21359198, 16828266, 12673792, 11727201, 31589614, 25525159) -
Pathogenic, criteria provided, single submitterclinical testingEurofins Ntd Llc (ga)Jan 10, 2018- -
Inborn genetic diseases Pathogenic:1
Pathogenic, criteria provided, single submitterclinical testingAmbry GeneticsNov 02, 2016The p.E72* pathogenic mutation (also known as c.214G>T), located in coding exon 3 of the CLN6 gene, results from a G to T substitution at nucleotide position 214. This changes the amino acid from a glutamic acid to a stop codon within coding exon 3. This mutation was first reported in the homozgyous state (referred to as G317T) in a child from Costa Rica with variant late infantile neuronal ceroid lipofuscinoses (Gao H et al. Am. J. Hum. Genet., 2002 Feb;70:324-35). In addition to the clinical data presented in the literature, this alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation. -
Neuronal ceroid lipofuscinosis Pathogenic:1
Pathogenic, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpDec 11, 2023This sequence change creates a premature translational stop signal (p.Glu72*) in the CLN6 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in CLN6 are known to be pathogenic (PMID: 19135028). This variant is present in population databases (rs104894483, gnomAD 0.05%). This premature translational stop signal has been observed in individuals with late-infantile neuronal ceroid lipofuscinosis (PMID: 11727201, 11791207, 12815591). This variant is also known as G317T. ClinVar contains an entry for this variant (Variation ID: 4077). For these reasons, this variant has been classified as Pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
0.34
D
BayesDel_noAF
Pathogenic
0.56
CADD
Pathogenic
39
DANN
Uncertain
0.99
Eigen
Pathogenic
0.88
Eigen_PC
Pathogenic
0.71
FATHMM_MKL
Uncertain
0.90
D
MutationTaster
Benign
1.0
A;A;A;A;D;D
Vest4
0.81
GERP RS
4.4
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.0

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.20
Details are displayed if max score is > 0.2
DS_AG_spliceai
0.20
Position offset: -3

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: rs104894483; hg19: chr15-68506711; API