NM_000195.5(HPS1):c.1473dup (p.Ser492fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 26, 2021
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV001992670.4

Allele description [Variation Report for NM_000195.5(HPS1):c.1473dup (p.Ser492fs)]

NM_000195.5(HPS1):c.1473dup (p.Ser492fs)

Gene:

HPS1:HPS1 biogenesis of lysosomal organelles complex 3 subunit 1 [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

10q24.2

Genomic location:

Preferred name:

NM_000195.5(HPS1):c.1473dup (p.Ser492fs)

HGVS:

NC_000010.11:g.98423816dup
NG_009646.1:g.28136dup
NM_000195.5:c.1473dupMANE SELECT
NM_001311345.2:c.501dup
NM_001322476.2:c.1473dup
NM_001322477.2:c.1473dup
NM_001322478.2:c.1374dup
NM_001322479.2:c.1374dup
NM_001322480.2:c.1212dup
NM_001322481.2:c.1212dup
NM_001322482.2:c.1113dup
NM_001322483.2:c.1104dup
NM_001322484.2:c.1104dup
NM_001322485.2:c.1005dup
NM_001322487.2:c.501dup
NM_001322489.2:c.501dup
NP_000186.2:p.Ser492fs
NP_001298274.1:p.Ser168fs
NP_001309405.1:p.Ser492fs
NP_001309406.1:p.Ser492fs
NP_001309407.1:p.Ser459fs
NP_001309408.1:p.Ser459fs
NP_001309409.1:p.Ser405fs
NP_001309410.1:p.Ser405fs
NP_001309411.1:p.Ser372fs
NP_001309412.1:p.Ser369fs
NP_001309413.1:p.Ser369fs
NP_001309414.1:p.Ser336fs
NP_001309416.1:p.Ser168fs
NP_001309418.1:p.Ser168fs
LRG_562t1:c.1473dup
LRG_562:g.28136dup
LRG_562p1:p.Ser492fs
NC_000010.10:g.100183568_100183569insG
NC_000010.10:g.100183573dup

Protein change:

S168fs

Links:

dbSNP: rs1278834481

NCBI 1000 Genomes Browser:

rs1278834481

Molecular consequence:

NM_000195.5:c.1473dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001311345.2:c.501dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322476.2:c.1473dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322477.2:c.1473dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322478.2:c.1374dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322479.2:c.1374dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322480.2:c.1212dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322481.2:c.1212dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322482.2:c.1113dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322483.2:c.1104dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322484.2:c.1104dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322485.2:c.1005dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322487.2:c.501dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322489.2:c.501dup - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002224717	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Aug 26, 2021)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 12442288, 16185271, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002224717

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Aug 26, 2021)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Hermansky-Pudlak syndrome type 1: gene organization, novel mutations, and clinical-molecular review of non-Puerto Rican cases.

Hermos CR, Huizing M, Kaiser-Kupfer MI, Gahl WA.

Hum Mutat. 2002 Dec;20(6):482.

PubMed [citation]

PMID:: 12442288

High frequency of Hermansky-Pudlak syndrome type 1 (HPS1) among Japanese albinism patients and functional analysis of HPS1 mutant protein.

Ito S, Suzuki T, Inagaki K, Suzuki N, Takamori K, Yamada T, Nakazawa M, Hatano M, Takiwaki H, Kakuta Y, Spritz RA, Tomita Y.

J Invest Dermatol. 2005 Oct;125(4):715-20.

PubMed [citation]

PMID:: 16185271

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002224717.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This sequence change creates a premature translational stop signal (p.Ser492Glnfs*90) 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 not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals affected with HPS1-related conditions. For these reasons, this variant has been classified as Pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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