rs1344658850
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PM5PP3_Moderate
The NM_017882.3(CLN6):c.506T>C(p.Leu169Pro) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,461,750 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 Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L169H) has been classified as Likely pathogenic.
Frequency
Consequence
NM_017882.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CLN6 | NM_017882.3 | c.506T>C | p.Leu169Pro | missense_variant | 5/7 | ENST00000249806.11 | |
CLN6 | NM_001411068.1 | c.602T>C | p.Leu201Pro | missense_variant | 5/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CLN6 | ENST00000249806.11 | c.506T>C | p.Leu169Pro | missense_variant | 5/7 | 1 | NM_017882.3 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250908Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135650
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461750Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 727172
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Ceroid lipofuscinosis, neuronal, 6A Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Counsyl | May 19, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at