rs58414354
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PM1PM2PM5PP3_StrongPP5
The NM_000421.5(KRT10):c.478T>G(p.Tyr160Asp) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Y160S) has been classified as Uncertain significance.
Frequency
Consequence
NM_000421.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KRT10 | NM_000421.5 | c.478T>G | p.Tyr160Asp | missense_variant | 1/8 | ENST00000269576.6 | |
KRT10-AS1 | NR_160888.1 | n.64+2900A>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KRT10 | ENST00000269576.6 | c.478T>G | p.Tyr160Asp | missense_variant | 1/8 | 1 | NM_000421.5 | P2 | |
KRT10-AS1 | ENST00000301665.9 | n.108+2900A>C | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome Cov.: 31
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Epidermolytic hyperkeratosis 2A, autosomal dominant Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Feb 01, 1994 | - - |
not provided Other:1
not provided, no classification provided | literature only | Epithelial Biology; Institute of Medical Biology, Singapore | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at