rs879255638
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM2PP3_StrongPP5
The NM_021619.3(PRDM12):c.866A>T(p.His289Leu) 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. 12/21 in silico tools predict a damaging 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. H289R) has been classified as Uncertain significance.
Frequency
Consequence
NM_021619.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRDM12 | NM_021619.3 | c.866A>T | p.His289Leu | missense_variant | 5/5 | ENST00000253008.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRDM12 | ENST00000253008.3 | c.866A>T | p.His289Leu | missense_variant | 5/5 | 1 | NM_021619.3 | P1 | |
PRDM12 | ENST00000676323.1 | c.866A>T | p.His289Leu | missense_variant | 5/6 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome Cov.: 31
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Congenital insensitivity to pain-hypohidrosis syndrome Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Aug 10, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at