NM_032383.5(HPS3):c.84_109del (p.Arg30fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Oct 23, 2022
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:: RCV002899250.2

Allele description [Variation Report for NM_032383.5(HPS3):c.84_109del (p.Arg30fs)]

NM_032383.5(HPS3):c.84_109del (p.Arg30fs)

Gene:

HPS3:HPS3 biogenesis of lysosomal organelles complex 2 subunit 1 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

3q24

Genomic location:

Preferred name:

NM_032383.5(HPS3):c.84_109del (p.Arg30fs)

HGVS:

NC_000003.12:g.149129807_149129832del
NG_009847.1:g.5224_5249del
NG_100910.1:g.228_253del
NM_001308258.2:c.84_109del
NM_032383.5:c.84_109delMANE SELECT
NP_001295187.1:p.Arg30fs
NP_115759.2:p.Arg30fs
LRG_563t1:c.84_109del
LRG_563:g.5224_5249del
LRG_563p1:p.Arg30fs
NC_000003.11:g.148847587_148847612del
NC_000003.11:g.148847594_148847619del

Protein change:

R30fs

Molecular consequence:

NM_001308258.2:c.84_109del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_032383.5:c.84_109del - 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
SCV003243821	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Oct 23, 2022)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 11590544, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003243821

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Oct 23, 2022)

germline

clinical testing

PubMed (2)
[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 3 in Ashkenazi Jews and other non-Puerto Rican patients with hypopigmentation and platelet storage-pool deficiency.

Huizing M, Anikster Y, Fitzpatrick DL, Jeong AB, D'Souza M, Rausche M, Toro JR, Kaiser-Kupfer MI, White JG, Gahl WA.

Am J Hum Genet. 2001 Nov;69(5):1022-32. Epub 2001 Oct 3.

PubMed [citation]

PMID:: 11590544
PMCID:: PMC1274349

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, SCV003243821.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with HPS3-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Arg30Leufs*42) in the HPS3 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in HPS3 are known to be pathogenic (PMID: 11590544).

#	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: Feb 20, 2024

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