rs28940896
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PM1PM2PM5PP3_StrongPP5
The NM_000226.4(KRT9):c.478C>T(p.Leu160Phe) 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. L160V) has been classified as Pathogenic.
Frequency
Consequence
NM_000226.4 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 |
---|---|---|---|---|---|---|---|
KRT9 | NM_000226.4 | c.478C>T | p.Leu160Phe | missense_variant | 1/8 | ENST00000246662.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KRT9 | ENST00000246662.9 | c.478C>T | p.Leu160Phe | missense_variant | 1/8 | 1 | NM_000226.4 | P1 | |
KRT9 | ENST00000588431.1 | c.-189-33C>T | intron_variant | 1 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD4 exome Cov.: 32
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
Epidermolytic palmoplantar keratoderma, 1 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jul 30, 2003 | - - |
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