U.S. flag

An official website of the United States government

NC_000003.12:g.(?_149129714)_(149129950_?)del AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Dec 17, 2019
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:
RCV000817930.2

Allele description [Variation Report for NC_000003.12:g.(?_149129714)_(149129950_?)del]

NC_000003.12:g.(?_149129714)_(149129950_?)del

Gene:
HPS3:HPS3 biogenesis of lysosomal organelles complex 2 subunit 1 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
3q24
Genomic location:
Preferred name:
NC_000003.12:g.(?_149129714)_(149129950_?)del
HGVS:
  • NC_000003.12:g.(?_149129714)_(149129950_?)del
  • NC_000003.11:g.(?_148847501)_(148847737_?)del

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: CN517202

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000958517Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Dec 17, 2019) 		germlineclinical testing

PubMed (2)
[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

Mutation of a new gene causes a unique form of Hermansky-Pudlak syndrome in a genetic isolate of central Puerto Rico.

Anikster Y, Huizing M, White J, Shevchenko YO, Fitzpatrick DL, Touchman JW, Compton JG, Bale SJ, Swank RT, Gahl WA, Toro JR.

Nat Genet. 2001 Aug;28(4):376-80.

PubMed [citation]
PMID:
11455388

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV000958517.2

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

Description

This variant is a gross deletion of the genomic region encompassing exon 1 of the HPS3 gene, which includes the initiator codon. The 5' end of this event is unknown as it extends beyond the assayed region for this gene and therefore may encompass additional genes. The 3' boundary is likely confined to intron 1 of the HPS3 gene. This is expected to result in an absent or disrupted protein product. A similar deletion of exon 1 has been observed to segregate with Hermansky-Pudlak syndrome in a family (PMID: 11455388). Loss-of-function variants in HPS3 are known to be pathogenic (PMID: 11590544). 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: Apr 23, 2022