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NC_000010.10:g.(?_100177321)_(101611388_?)del AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Sep 15, 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:
RCV001983006.2

Allele description

NC_000010.10:g.(?_100177321)_(101611388_?)del

Genes:
  • ABCC2:ATP binding cassette subfamily C member 2 [Gene - OMIM - HGNC]
  • HPS1:HPS1 biogenesis of lysosomal organelles complex 3 subunit 1 [Gene - OMIM - HGNC]
  • NKX2-3:NK2 homeobox 3 [Gene - OMIM - HGNC]
  • CUTC:cutC copper transporter [Gene - OMIM - HGNC]
  • CNNM1:cyclin and CBS domain divalent metal cation transport mediator 1 [Gene - OMIM - HGNC]
  • COX15:cytochrome c oxidase assembly homolog COX15 [Gene - OMIM - HGNC]
  • ENTPD7:ectonucleoside triphosphate diphosphohydrolase 7 [Gene - OMIM - HGNC]
  • GOT1:glutamic-oxaloacetic transaminase 1 [Gene - OMIM - HGNC]
  • HPSE2:heparanase 2 (inactive) [Gene - OMIM - HGNC]
  • SLC25A28:solute carrier family 25 member 28 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
10q24.2
Genomic location:
Chr10: 100177321 - 101611388 (on Assembly GRCh37)
Preferred name:
NC_000010.10:g.(?_100177321)_(101611388_?)del
HGVS:
NC_000010.10:g.(?_100177321)_(101611388_?)del

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: CN517202

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002241432Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Sep 15, 2021) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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 Invitae, SCV002241432.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

A gross deletion of the genomic region encompassing the full coding sequence of the HPS1 gene has been identified. Loss-of-function variants in HPS1 are known to be pathogenic (PMID: 12442288, 16185271). The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. 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.

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

Last Updated: Feb 13, 2023