NM_000195.5(HPS1):c.692C>T (p.Pro231Leu) AND Hermansky-Pudlak syndrome 1

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Feb 17, 2022
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000366388.6

Allele description [Variation Report for NM_000195.5(HPS1):c.692C>T (p.Pro231Leu)]

NM_000195.5(HPS1):c.692C>T (p.Pro231Leu)

Gene:

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

Variant type:

single nucleotide variant

Cytogenetic location:

10q24.2

Genomic location:

Preferred name:

NM_000195.5(HPS1):c.692C>T (p.Pro231Leu)

HGVS:

NC_000010.11:g.98430647G>A
NG_009646.1:g.21301C>T
NM_000195.5:c.692C>TMANE SELECT
NM_001311345.2:c.-182C>T
NM_001322476.2:c.692C>T
NM_001322477.2:c.692C>T
NM_001322478.2:c.692C>T
NM_001322479.2:c.692C>T
NM_001322480.2:c.431C>T
NM_001322481.2:c.431C>T
NM_001322482.2:c.431C>T
NM_001322483.2:c.323C>T
NM_001322484.2:c.323C>T
NM_001322485.2:c.323C>T
NM_001322487.2:c.-281C>T
NM_001322489.2:c.-182C>T
NM_001322490.2:c.574C>T
NM_001322491.2:c.692C>T
NM_001322492.2:c.574C>T
NM_182639.4:c.692C>T
NP_000186.2:p.Pro231Leu
NP_001309405.1:p.Pro231Leu
NP_001309406.1:p.Pro231Leu
NP_001309407.1:p.Pro231Leu
NP_001309408.1:p.Pro231Leu
NP_001309409.1:p.Pro144Leu
NP_001309410.1:p.Pro144Leu
NP_001309411.1:p.Pro144Leu
NP_001309412.1:p.Pro108Leu
NP_001309413.1:p.Pro108Leu
NP_001309414.1:p.Pro108Leu
NP_001309419.1:p.Arg192Trp
NP_001309420.1:p.Pro231Leu
NP_001309421.1:p.Arg192Trp
NP_872577.1:p.Pro231Leu
LRG_562t1:c.692C>T
LRG_562:g.21301C>T
LRG_562p1:p.Pro231Leu
NC_000010.10:g.100190404G>A
NM_000195.3:c.692C>T

Protein change:

P108L

Links:

dbSNP: rs773953162

NCBI 1000 Genomes Browser:

rs773953162

Molecular consequence:

NM_001311345.2:c.-182C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322487.2:c.-281C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322489.2:c.-182C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_000195.5:c.692C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001322476.2:c.692C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001322477.2:c.692C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001322478.2:c.692C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001322479.2:c.692C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001322480.2:c.431C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001322481.2:c.431C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001322482.2:c.431C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001322483.2:c.323C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001322484.2:c.323C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001322485.2:c.323C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001322490.2:c.574C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001322491.2:c.692C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001322492.2:c.574C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_182639.4:c.692C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Hermansky-Pudlak syndrome 1 (HPS1)
Synonyms:: DELTA STORAGE POOL DISEASE
Identifiers:: MONDO: MONDO:0008748; MedGen: C2931875; Orphanet: 231500; Orphanet: 79430; OMIM: 203300

Recent activity

Clear Turn Off Turn On

znrf3 [Perca flavescens]
znrf3 [Perca flavescens]
Gene ID:114555561

Gene

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000359666	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Uncertain significance (Jan 12, 2018)	germline	clinical testing	Citation Link,
SCV002801362	Fulgent Genetics, Fulgent Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Feb 17, 2022)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000359666

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)

Uncertain significance
(Jan 12, 2018)

germline

clinical testing

Citation Link,

SCV002801362

Fulgent Genetics, Fulgent Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Feb 17, 2022)

unknown

clinical testing

PubMed (1)
[See all records that cite this PMID]

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
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Illumina Laboratory Services, Illumina, SCV000359666.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.

#	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

From Fulgent Genetics, Fulgent Genetics, SCV002801362.1

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

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

Last Updated: Sep 29, 2024

ClinVar

Relating variation to medicine