rs281865076
Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong
The NM_000195.5(HPS1):c.391C>T(p.Arg131Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000248 in 1,613,924 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_000195.5 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HPS1 | NM_000195.5 | c.391C>T | p.Arg131Ter | stop_gained | 5/20 | ENST00000361490.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HPS1 | ENST00000361490.9 | c.391C>T | p.Arg131Ter | stop_gained | 5/20 | 1 | NM_000195.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152108Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251160Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135774
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461816Hom.: 0 Cov.: 32 AF XY: 0.00000275 AC XY: 2AN XY: 727194
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152108Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74304
ClinVar
Submissions by phenotype
Hermansky-Pudlak syndrome 1 Pathogenic:3
Pathogenic, criteria provided, single submitter | clinical testing | Johns Hopkins Genomics, Johns Hopkins University | Oct 20, 2021 | HPS1 c.391C>T has been reported in multiple individuals with Hermansky-Pudlak syndrome 1. This variant (rs281865076) is rare (<0.1%) in a large population dataset (gnomAD: 1/251160 total alleles; 0.0004%; no homozygotes) and has been reported in ClinVar. This nonsense variant results in a premature stop codon in exon 5 likely leading to nonsense-mediated decay and lack of protein production. We consider HPS1 c.391C>T to be pathogenic. - |
Pathogenic, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Aug 03, 2021 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Baylor Genetics | Aug 28, 2023 | - - |
Hermansky-Pudlak syndrome Pathogenic:2
Pathogenic, criteria provided, single submitter | curation | Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard | Nov 29, 2021 | The p.Arg131Ter variant in HPS1 has been reported in 2 individuals with Hermansky-Pudlak syndrome (PMID: 14510955, 21458243), and has been identified in 0.003% (1/34584) of Latino/Admixed American chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP ID: rs281865076). Although this variant has been seen in the general population in a heterozygous state, its frequency is low enough to be consistent with a recessive carrier frequency. This variant was found to be de novo in 1 individual with confirmed paternity and maternity (PMID: 14510955). Of the 2 affected individuals, 1 was a compound heterozygote that carried a reported pathogenic variant in trans, which increases the likelihood that the p.Arg131Ter variant is pathogenic (VariationID: 5278; PMID: 14510955). This variant has also been reported in ClinVar (Variation ID#: 21104) and has been interpreted as pathogenic by GeneReviews and Invitae. In vitro functional studies provide some evidence that the p.Arg131Ter variant may impact protein function (PMID: 14510955). However, these types of assays may not accurately represent biological function. This nonsense variant leads to a premature termination codon at position 131, which is predicted to lead to a truncated or absent protein. Loss of function of the HPS1 gene is an established disease mechanism in autosomal recessive Hermansky-Pudlak syndrome. In summary, this variant meets criteria to be classified as pathogenic for autosomal recessive Hermansky-Pudlak syndrome. ACMG/AMP Criteria applied: PM3, PM2_supporting, PVS1, PS3_moderate, PS2 (Richards 2015). - |
Pathogenic, no assertion criteria provided | clinical testing | Natera, Inc. | Oct 11, 2021 | - - |
not provided Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | Nov 04, 2023 | This sequence change creates a premature translational stop signal (p.Arg131*) in the HPS1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in HPS1 are known to be pathogenic (PMID: 12442288, 16185271). This variant is present in population databases (rs281865076, gnomAD 0.003%). This premature translational stop signal has been observed in individuals with HPS1-related conditions (PMID: 14510955, 21458243). ClinVar contains an entry for this variant (Variation ID: 21104). For these reasons, this variant has been classified as Pathogenic. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at