chr17-40866768-A-C
Variant summary
Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PM2PM5PP3_StrongPP5
The NM_000223.4(KRT12):c.419T>G(p.Leu140Arg) 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. L140Q) has been classified as Likely pathogenic.
Frequency
Consequence
NM_000223.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KRT12 | NM_000223.4 | c.419T>G | p.Leu140Arg | missense_variant | 1/8 | ENST00000251643.5 | NP_000214.1 | |
LOC105371777 | XR_934754.3 | n.63+15908A>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KRT12 | ENST00000251643.5 | c.419T>G | p.Leu140Arg | missense_variant | 1/8 | 1 | NM_000223.4 | ENSP00000251643.4 | ||
KRT12 | ENST00000647902.1 | c.311T>G | p.Leu104Arg | missense_variant | 2/4 | ENSP00000497770.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 34
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Corneal dystrophy, Meesmann, 1 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Dec 01, 1997 | - - |
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