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
Consequence
ENST00000249806.11 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CLN6 | NM_017882.3 | c.214G>T | p.Glu72Ter | stop_gained | 3/7 | ENST00000249806.11 | NP_060352.1 | |
CLN6 | NM_001411068.1 | c.310G>T | p.Glu104Ter | stop_gained | 3/7 | NP_001397997.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CLN6 | ENST00000249806.11 | c.214G>T | p.Glu72Ter | stop_gained | 3/7 | 1 | NM_017882.3 | ENSP00000249806 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000230 AC: 35AN: 152218Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000676 AC: 17AN: 251428Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135902
GnomAD4 exome AF: 0.0000151 AC: 22AN: 1461396Hom.: 0 Cov.: 30 AF XY: 0.0000124 AC XY: 9AN XY: 727032
GnomAD4 genome AF: 0.000230 AC: 35AN: 152218Hom.: 0 Cov.: 33 AF XY: 0.000403 AC XY: 30AN XY: 74362
ClinVar
Submissions by phenotype
Ceroid lipofuscinosis, neuronal, 6A Pathogenic:2Other:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Feb 01, 2002 | - - |
not provided, no classification provided | literature only | GeneReviews | - | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Counsyl | Mar 12, 2018 | - - |
not provided Pathogenic:2
Pathogenic, criteria provided, single submitter | clinical testing | GeneDx | May 03, 2022 | Nonsense 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 submitter | clinical testing | Eurofins Ntd Llc (ga) | Jan 10, 2018 | - - |
Inborn genetic diseases Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 02, 2016 | The 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 submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 11, 2023 | This 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:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at