rs281865082

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Pathogenic. The variant received 16 ACMG points: 16P and 0B. PVS1PP5_Very_Strong

The NM_000195.5(HPS1):c.972delC(p.Met325TrpfsTer6) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000534 in 1,535,616 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (★★). Synonymous variant affecting the same amino acid position (i.e. P324P) has been classified as Likely benign. Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: 𝑓 0.00012 ( 0 hom., cov: 33)

Exomes 𝑓: 0.000046 ( 0 hom. )

Consequence

HPS1
NM_000195.5 frameshift

Scores

Not classified

Clinical Significance

Pathogenic criteria provided, multiple submitters, no conflicts P:11O:1

Conservation

PhyloP100: 0.721

Publications

18 publications found

Variant links:

Genes affected

HPS1 (HGNC:5163): (HPS1 biogenesis of lysosomal organelles complex 3 subunit 1) This gene encodes a protein that may play a role in organelle biogenesis associated with melanosomes, platelet dense granules, and lysosomes. The encoded protein is a component of three different protein complexes termed biogenesis of lysosome-related organelles complex (BLOC)-3, BLOC4, and BLOC5. Mutations in this gene are associated with Hermansky-Pudlak syndrome type 1. Alternative splicing results in multiple transcript variants. A pseudogene related to this gene is located on chromosome 22. [provided by RefSeq, Aug 2015]

HPS1 Gene-Disease associations (from GenCC):

Hermansky-Pudlak syndrome 1
Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: G2P, ClinGen, Labcorp Genetics (formerly Invitae)
Hermansky-Pudlak syndrome with pulmonary fibrosis
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

HPS1 links:

ENSG00000289758 (HGNC:):

ENSG00000289758 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Pathogenic. The variant received 16 ACMG points.

PVS1

Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.

PP5

Variant 10-98427229-TG-T is Pathogenic according to our data. Variant chr10-98427229-TG-T is described in ClinVar as Pathogenic. ClinVar VariationId is 5280.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HPS1	NM_000195.5 link	c.972delC	p.Met325TrpfsTer6	frameshift_variant	Exon 11 of 20	ENST00000361490.9	NP_000186.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein
HPS1	ENST00000361490.9 link	c.972delC	p.Met325TrpfsTer6	frameshift_variant	Exon 11 of 20	1	NM_000195.5	ENSP00000355310.4
ENSG00000289758	ENST00000699159.1 link	n.*331delC		non_coding_transcript_exon_variant	Exon 10 of 24			ENSP00000514167.1
ENSG00000289758	ENST00000699159.1 link	n.*331delC		3_prime_UTR_variant	Exon 10 of 24			ENSP00000514167.1

Frequencies

GnomAD3 genomes

AF:

0.000125

AC:

AN:

151930

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000266

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.000472

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000442

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.000166

AC:

AN:

144354

AF XY:

0.000118

show subpopulations

Gnomad AFR exome

AF:

0.000246

Gnomad AMR exome

AF:

0.000132

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.000288

Gnomad FIN exome

AF:

0.000857

Gnomad NFE exome

AF:

0.0000714

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000455

AC:

AN:

1383570

Hom.:

Cov.:

AF XY:

0.0000425

AC XY:

AN XY:

682764

show subpopulations

African (AFR)

AF:

0.0000966

AC:

AN:

31044

American (AMR)

AF:

0.0000566

AC:

AN:

35310

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

24906

East Asian (EAS)

AF:

0.0000848

AC:

AN:

35386

South Asian (SAS)

AF:

0.0000383

AC:

AN:

78382

European-Finnish (FIN)

AF:

0.000578

AC:

AN:

48406

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5646

European-Non Finnish (NFE)

AF:

0.0000225

AC:

AN:

1067228

Other (OTH)

AF:

0.00

AC:

AN:

57262

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.434

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.000125

AC:

AN:

152046

Hom.:

Cov.:

AF XY:

0.000175

AC XY:

AN XY:

74330

show subpopulations

African (AFR)

AF:

0.000265

AC:

AN:

41508

American (AMR)

AF:

0.00

AC:

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3468

East Asian (EAS)

AF:

0.00

AC:

AN:

5154

South Asian (SAS)

AF:

0.00

AC:

AN:

4826

European-Finnish (FIN)

AF:

0.000472

AC:

AN:

10584

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0000442

AC:

AN:

67916

Other (OTH)

AF:

0.00

AC:

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.491

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00116

Hom.:

Bravo

AF:

0.0000567

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:11Other:1

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Hermansky-Pudlak syndrome 1

Pathogenic:6Other:1

Mar 01, 1998

OMIM

Significance:Pathogenic

Review Status:no assertion criteria provided

Collection Method:literature only

- -

Jul 26, 2024

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Significance:Pathogenic

Review Status:criteria provided, single submitter

Collection Method:clinical testing

The HPS1 c.972del; p.Met325TrpfsTer6 variant (rs281865082, ClinVar Variation ID: 5280) is reported compound heterozygous in the literature in multiple individuals affected with Hermansky-Pudlak syndrome (Liu 2021, O’Brien 2021). This variant is found in the general population with an overall allele frequency of 0.02% (28/175,586 alleles) in the Genome Aggregation Database (v2.1.1), but is considered a low confidence variant in the database. This variant causes a frameshift by deleting a single nucleotide, so it is predicted to result in a truncated protein or mRNA subject to nonsense-mediated decay. Based on available information, this variant is considered to be pathogenic. References: Liu T et al. Genetic variants and mutational spectrum of Chinese Hermansky-Pudlak syndrome patients. Pigment Cell Melanoma Res. 2021 Jan;34(1):111-121. PMID: 32725903. O'Brien KJ et al. Inflammatory bowel disease in Hermansky-Pudlak syndrome: a retrospective single-centre cohort study. J Intern Med. 2021 Jul;290(1):129-140. PMID: 33423334. -

Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India

Significance:Pathogenic

Review Status:criteria provided, single submitter

Collection Method:research

A known frameshift deletion, c.972del in exon 11 of HPS1 was observed in homozygous state in proband. (Thuong et al., 2022; VCV000005280.25). Sanger validation and segregation analysis showed that the variant was present in homozygous state in the proband and in heterozygous state in the mother and the father. The variant is absent in homozygous state in gnomAD (v4.1.0) and our inhouse database. The variant is present in heterozygous state in 82 individuals in gnomAD (v4.1.0) and 8 individuals in our in-house database of 3728 exomes. This variant is predicted to cause a shift in the reading frame of the transcript which will either lead to nonsense-mediated mRNA decay or formation of a truncated product. -

Mar 08, 2024

Fulgent Genetics, Fulgent Genetics

Significance:Pathogenic

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

GeneReviews

Significance:not provided

Review Status:no classification provided

Collection Method:literature only

- -

Feb 14, 2024

Baylor Genetics

Significance:Pathogenic

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Jun 10, 2021

Genome-Nilou Lab

Significance:Pathogenic

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

not provided

Pathogenic:2

Aug 28, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Pathogenic

Review Status:criteria provided, single submitter

Collection Method:clinical testing

This sequence change creates a premature translational stop signal (p.Met325Trpfs*6) 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). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This premature translational stop signal has been observed in individuals with Hermansky‚ÄìPudlak syndrome (PMID: 19334085, 27593200). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 5280). For these reasons, this variant has been classified as Pathogenic. -

Jul 09, 2019

Genetic Services Laboratory, University of Chicago

Significance:Pathogenic

Review Status:criteria provided, single submitter

Collection Method:clinical testing

DNA sequence analysis of the HPS1 gene demonstrated a one base pair deletion in exon 11, c.972del. This sequence change results in an amino acid frameshift and creates a premature stop codon 5 amino acids downstream of the sequence change, p.Met325Trpfs*6. This sequence change is predicted to result in an abnormal transcript, which may be degraded, or may lead to the production of a truncated HPS1 protein with potentially abnormal function. This sequence change has been described in the gnomAD database with a population frequency of 0.012% in African subpopulation (dbSNP rs281865082). This sequence change has previously been described in patients with Hermansky-Pudlak syndrome in both homozygous and compound heterozygous states (PMID: 20662851, PMID: 19334085, PMID: 8896559). Functional studies have shown results that suggest a lack of function of the protein (PMID: 21833017). These collective evidences indicate that this sequence change is pathogenic. -

Hermansky-Pudlak syndrome

Pathogenic:2

Nov 29, 2021

Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard

Significance:Pathogenic

Review Status:criteria provided, single submitter

Collection Method:curation

The p.Met325fs (c.972del) variant in HPS1 has been reported in at least 4 individuals with Hermansky-Pudlak syndrome (PMID: 27593200, 19334085, 9705234, 9497254), segregated with disease in 2 affected relatives from 2 families (PMID: 19334085, 9705234) and has been identified in 0.09% (15/17454) of European (Finnish) chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP ID: rs281865083). Although this variant has been seen in the general population in a heterozygous state, its frequency is not high enough to rule out a pathogenic role. It is of note that this variant occurs in a homopolymer repeat, which could indicate that it exists as an artifact from sequencing. However, disease-causing variants have been reported in homopolymer regions, so this is not enough to rule out a pathogenic role. Of the 4 affected individuals, 1 was compound heterozygote that carried a reported pathogenic variant in trans, which increases the likelihood that the p.Met325fs variant is pathogenic (VariationID: 21091; PMID: 9705234). This variant has also been reported in ClinVar (Variation ID#: 5280) and has been interpreted as pathogenic by Invitae, Nilou-Genome Lab, OMIM, Natera, Inc., and GeneReviews. In vitro functional studies provide some evidence that the p.Met325fs variant may impact protein function (PMID: 9705234). However, these types of assays may not accurately represent biological function. This variant is predicted to cause a frameshift, which alters the protein’s amino acid sequence beginning at position 325 and leads to a premature termination codon 6 amino acids downstream. This alteration is then 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, PP1, PVS1 , PS3_moderate (Richards 2015). -

Sep 16, 2020

Natera, Inc.

Significance:Pathogenic

Review Status:no assertion criteria provided

Collection Method:clinical testing

- -

HPS1-related disorder

Pathogenic:1

Sep 28, 2024

PreventionGenetics, part of Exact Sciences

Significance:Pathogenic

Review Status:no assertion criteria provided

Collection Method:clinical testing

The HPS1 c.972delC variant is predicted to result in a frameshift and premature protein termination (p.Met325Trpfs*6). This variant has reported in multiple individuals with Hermansky-Pudlak syndrome (Wei et al. 2016. PubMed ID: 27593200, Table S2, Liu et al. 2020. PubMed ID: 32725903). This variant is reported in 0.086% of alleles in individuals of European (Finnish) descent in gnomAD. Frameshift variants in HPS1 are expected to be pathogenic. This variant is interpreted as pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.72

Mutation Taster

=0/200

disease causing (ClinVar)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over