chr11-18296891-G-A
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_181507.2(HPS5):c.1417C>T(p.Gln473Ter) variant causes a stop gained 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 (★). Synonymous variant affecting the same amino acid position (i.e. Q473Q) has been classified as Likely benign. Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_181507.2 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HPS5 | NM_181507.2 | c.1417C>T | p.Gln473Ter | stop_gained | 12/23 | ENST00000349215.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HPS5 | ENST00000349215.8 | c.1417C>T | p.Gln473Ter | stop_gained | 12/23 | 1 | NM_181507.2 | P1 | |
HPS5 | ENST00000396253.7 | c.1075C>T | p.Gln359Ter | stop_gained | 11/22 | 1 | |||
HPS5 | ENST00000438420.6 | c.1075C>T | p.Gln359Ter | stop_gained | 11/22 | 1 | |||
HPS5 | ENST00000531848.1 | c.1075C>T | p.Gln359Ter | stop_gained | 11/11 | 5 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 30
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Hermansky-Pudlak syndrome 5 Pathogenic:1
Pathogenic, no assertion criteria provided | clinical testing | Laboratoire de Génétique Moléculaire, CHU Bordeaux | Mar 14, 2017 | - - |
not provided Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Feb 01, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at