chr19-50908611-C-A
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_004917.5(KLK4):c.443G>T(p.Cys148Phe) variant causes a missense change. 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 Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. C148Y) has been classified as Uncertain significance.
Frequency
Consequence
NM_004917.5 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 |
---|---|---|---|---|---|---|---|
KLK4 | NM_004917.5 | c.443G>T | p.Cys148Phe | missense_variant | 4/6 | ENST00000324041.6 | |
KLK4 | NM_001302961.2 | c.158G>T | p.Cys53Phe | missense_variant | 3/5 | ||
KLK4 | XM_011527545.4 | c.443G>T | p.Cys148Phe | missense_variant | 3/4 | ||
KLK4 | NR_126566.2 | n.436G>T | non_coding_transcript_exon_variant | 3/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KLK4 | ENST00000324041.6 | c.443G>T | p.Cys148Phe | missense_variant | 4/6 | 1 | NM_004917.5 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD4 exome Cov.: 32
GnomAD4 genome ? Cov.: 31
ClinVar
Submissions by phenotype
Amelogenesis imperfecta type 2A1 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Reference Center For Rare Oral And Dental Diseases, Crmr O-rares, Hôpitaux Universitaires De Strasbourg | Mar 01, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.