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NM_000195.5(HPS1):c.988-1G>T AND Hermansky-Pudlak syndrome 1

Germline classification:
Pathogenic (3 submissions)
Last evaluated:
Jan 16, 2024
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:
RCV003469730.5

Allele description [Variation Report for NM_000195.5(HPS1):c.988-1G>T]

NM_000195.5(HPS1):c.988-1G>T

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.988-1G>T
HGVS:
  • NC_000010.11:g.98425986C>A
  • NG_009646.1:g.25962G>T
  • NM_000195.5:c.988-1G>TMANE SELECT
  • NM_001311345.2:c.16-1G>T
  • NM_001322476.2:c.988-1G>T
  • NM_001322477.2:c.988-1G>T
  • NM_001322478.2:c.889-1G>T
  • NM_001322479.2:c.889-1G>T
  • NM_001322480.2:c.727-1G>T
  • NM_001322481.2:c.727-1G>T
  • NM_001322482.2:c.628-1G>T
  • NM_001322483.2:c.619-1G>T
  • NM_001322484.2:c.619-1G>T
  • NM_001322485.2:c.520-1G>T
  • NM_001322487.2:c.16-1G>T
  • NM_001322489.2:c.16-1G>T
  • LRG_562t1:c.988-1G>T
  • LRG_562:g.25962G>T
  • NC_000010.10:g.100185743C>A
  • NM_000195.4:c.988-1G>T
Links:
dbSNP: rs764927038
NCBI 1000 Genomes Browser:
rs764927038
Molecular consequence:
  • NM_000195.5:c.988-1G>T - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001311345.2:c.16-1G>T - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322476.2:c.988-1G>T - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322477.2:c.988-1G>T - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322478.2:c.889-1G>T - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322479.2:c.889-1G>T - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322480.2:c.727-1G>T - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322481.2:c.727-1G>T - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322482.2:c.628-1G>T - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322483.2:c.619-1G>T - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322484.2:c.619-1G>T - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322485.2:c.520-1G>T - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322487.2:c.16-1G>T - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322489.2:c.16-1G>T - splice acceptor variant - [Sequence Ontology: SO:0001574]

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

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV004199937Baylor Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Jan 16, 2024)
unknownclinical testing

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

SCV004236190Revvity Omics, Revvity
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(May 3, 2023)
germlineclinical testing

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

SCV005086550Victorian Clinical Genetics Services, Murdoch Childrens Research Institute

See additional submitters

criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Jul 16, 2023)
germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Hermansky-Pudlak syndrome type 1 in patients of Indian descent.

Vincent LM, Adams D, Hess RA, Ziegler SG, Tsilou E, Golas G, O'Brien KJ, White JG, Huizing M, Gahl WA.

Mol Genet Metab. 2009 Jul;97(3):227-33. doi: 10.1016/j.ymgme.2009.03.011. Epub 2009 Apr 2.

PubMed [citation]
PMID:
19398212
PMCID:
PMC2694228

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 Baylor Genetics, SCV004199937.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From Revvity Omics, Revvity, SCV004236190.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, SCV005086550.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with Hermansky-Pudlak syndrome 1 (MIM#203300). (I) 0106 - This gene is associated with autosomal recessive disease. (I) 0210 - Splice site variant proven to affect splicing of the transcript with a known effect on protein sequence. RT-PCR on patient melanocytes has confirmed the inframe skipping of exon 12 (PMID: 19398212). (SP) 0252 - This variant is homozygous. However, there appears to be an overlapping deletion. (I) 0304 - Variant is present in gnomAD (v2) <0.01 for a recessive condition (3 heterozygotes, 0 homozygotes). (SP) 0600 - Variant affects part of the Fuz_longin_2 domain (DECIPHER). (I) 0705 - No comparable splice variants have previous evidence for pathogenicity. (I) 0802 - This variant has moderate previous evidence of pathogenicity in unrelated individuals. This variant has been reported as likely pathogenic and pathogenic (ClinVar), and observed in a homozygous individual with Hermansky-Pudlak syndrome (PMID: 19398212). (SP) 0905 - No published segregation evidence has been identified for this variant. (I) 1206 - This variant has been shown to be paternally inherited (by trio analysis). (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Jul 23, 2024