NM_181507.2(HPS5):c.2949_2950insTA (p.Gly984Ter) AND not provided

This record was updated by the submitter. Please see the current version.

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jul 26, 2023
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:: RCV003560673.1

Allele description

NM_181507.2(HPS5):c.2949_2950insTA (p.Gly984Ter)

Gene:

HPS5:HPS5 biogenesis of lysosomal organelles complex 2 subunit 2 [Gene - OMIM - HGNC]

Variant type:

Insertion

Cytogenetic location:

11p15.1

Genomic location:

Preferred name:

NM_181507.2(HPS5):c.2949_2950insTA (p.Gly984Ter)

HGVS:

NC_000011.10:g.18285347_18285348insTA
NG_008877.1:g.41827_41828insTA
NM_007216.4:c.2607_2608insTA
NM_181507.2:c.2949_2950insTAMANE SELECT
NM_181508.1:c.2607_2608insTA
NP_009147.3:p.Gly870Ter
NP_852608.1:p.Gly984Ter
NP_852608.1:p.Gly984Terfs
NP_852609.1:p.Gly870Ter
LRG_586t1:c.2949_2950insTA
LRG_586:g.41827_41828insTA
LRG_586p1:p.Gly984Terfs
NC_000011.9:g.18306894_18306895insTA
NM_181507.1:c.2949_2950insTA

Protein change:

G870*

Molecular consequence:

NM_007216.4:c.2607_2608insTA - nonsense - [Sequence Ontology: SO:0001587]
NM_181507.2:c.2949_2950insTA - nonsense - [Sequence Ontology: SO:0001587]
NM_181508.1:c.2607_2608insTA - nonsense - [Sequence Ontology: SO:0001587]

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
SCV004307542	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jul 26, 2023)	germline	clinical testing	PubMed (5) [See all records that cite these PMIDs] 12548288, 15296495, 21833017, 26785811, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004307542

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jul 26, 2023)

germline

clinical testing

PubMed (5)
[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

Ru2 and Ru encode mouse orthologs of the genes mutated in human Hermansky-Pudlak syndrome types 5 and 6.

Zhang Q, Zhao B, Li W, Oiso N, Novak EK, Rusiniak ME, Gautam R, Chintala S, O'Brien EP, Zhang Y, Roe BA, Elliott RW, Eicher EM, Liang P, Kratz C, Legius E, Spritz RA, O'Sullivan TN, Copeland NG, Jenkins NA, Swank RT.

Nat Genet. 2003 Feb;33(2):145-53. Epub 2003 Jan 27.

PubMed [citation]

PMID:: 12548288

Cellular, molecular and clinical characterization of patients with Hermansky-Pudlak syndrome type 5.

Huizing M, Hess R, Dorward H, Claassen DA, Helip-Wooley A, Kleta R, Kaiser-Kupfer MI, White JG, Gahl WA.

Traffic. 2004 Sep;5(9):711-22.

PubMed [citation]

PMID:: 15296495

See all PubMed Citations (5)

Details of each submission

From Invitae, SCV004307542.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (5)

Description

For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with HPS5-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Gly984*) in the HPS5 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in HPS5 are known to be pathogenic (PMID: 12548288, 15296495, 21833017, 26785811).

#	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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