15-68086598-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PP3PP5
The NM_016166.3(PIAS1):c.317C>T(p.Ser106Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000013 in 1,613,780 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (no stars). Synonymous variant affecting the same amino acid position (i.e. S106S) has been classified as Benign.
Frequency
Consequence
NM_016166.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PIAS1 | NM_016166.3 | c.317C>T | p.Ser106Leu | missense_variant | 2/14 | ENST00000249636.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PIAS1 | ENST00000249636.11 | c.317C>T | p.Ser106Leu | missense_variant | 2/14 | 1 | NM_016166.3 | P1 | |
PIAS1 | ENST00000545237.1 | c.323C>T | p.Ser108Leu | missense_variant | 3/15 | 2 | |||
PIAS1 | ENST00000564915.5 | c.317C>T | p.Ser106Leu | missense_variant, NMD_transcript_variant | 2/5 | 5 | |||
PIAS1 | ENST00000562190.1 | c.*407C>T | 3_prime_UTR_variant, NMD_transcript_variant | 4/6 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152156Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000161 AC: 4AN: 249158Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135158
GnomAD4 exome AF: 0.0000116 AC: 17AN: 1461624Hom.: 1 Cov.: 31 AF XY: 0.0000124 AC XY: 9AN XY: 727090
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152156Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74330
ClinVar
Submissions by phenotype
Nephronophthisis Pathogenic:1
Likely pathogenic, no assertion criteria provided | literature only | Yale Center for Mendelian Genomics, Yale University | Dec 23, 2015 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at