NC_000005.9:g.(?_76115008)_(78281071_?)del AND Hermansky-Pudlak syndrome 2

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Mar 6, 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:: RCV003113301.5

Allele description [Variation Report for NC_000005.9:g.(?_76115008)_(78281071_?)del]

NC_000005.9:g.(?_76115008)_(78281071_?)del

Genes:

F2RL1:F2R like trypsin receptor 1 [Gene - OMIM - HGNC]
LHFPL2:LHFPL tetraspan subfamily member 2 [Gene - OMIM - HGNC]
S100Z:S100 calcium binding protein Z [Gene - OMIM - HGNC]
WDR41:WD repeat domain 41 [Gene - OMIM - HGNC]
AP3B1:adaptor related protein complex 3 subunit beta 1 [Gene - OMIM - HGNC]
AGGF1:angiogenic factor with G-patch and FHA domains 1 [Gene - OMIM - HGNC]
ARSB:arylsulfatase B [Gene - OMIM - HGNC]
CRHBP:corticotropin releasing hormone binding protein [Gene - OMIM - HGNC]
OTP:orthopedia homeobox [Gene - OMIM - HGNC]
PDE8B:phosphodiesterase 8B [Gene - OMIM - HGNC]
SCAMP1:secretory carrier membrane protein 1 [Gene - OMIM - HGNC]
TBCA:tubulin folding cofactor A [Gene - OMIM - HGNC]
ZBED3:zinc finger BED-type containing 3 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

5q13.3-14.1

Genomic location:

Chr5: 76115008 - 78281071 (on Assembly GRCh37)

Preferred name:

NC_000005.9:g.(?_76115008)_(78281071_?)del

HGVS:

NC_000005.9:g.(?_76115008)_(78281071_?)del

Condition(s)

Name:: Hermansky-Pudlak syndrome 2 (HPS2)
Synonyms:: Platelet defects and oculocutaneous albinism
Identifiers:: MONDO: MONDO:0011997; MedGen: C1842362; Orphanet: 79430; OMIM: 608233

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003791388	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Mar 6, 2022)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 16507770, 23403622, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003791388

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Mar 6, 2022)

germline

clinical testing

PubMed (3)
[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

Innate immunity defects in Hermansky-Pudlak type 2 syndrome.

Fontana S, Parolini S, Vermi W, Booth S, Gallo F, Donini M, Benassi M, Gentili F, Ferrari D, Notarangelo LD, Cavadini P, Marcenaro E, Dusi S, Cassatella M, Facchetti F, Griffiths GM, Moretta A, Notarangelo LD, Badolato R.

Blood. 2006 Jun 15;107(12):4857-64. Epub 2006 Feb 28.

PubMed [citation]

PMID:: 16507770

The risk of hemophagocytic lymphohistiocytosis in Hermansky-Pudlak syndrome type 2.

Jessen B, Bode SF, Ammann S, Chakravorty S, Davies G, Diestelhorst J, Frei-Jones M, Gahl WA, Gochuico BR, Griese M, Griffiths G, Janka G, Klein C, Kögl T, Kurnik K, Lehmberg K, Maul-Pavicic A, Mumford AD, Pace D, Parvaneh N, Rezaei N, de Saint Basile G, et al.

Blood. 2013 Apr 11;121(15):2943-51. doi: 10.1182/blood-2012-10-463166. Epub 2013 Feb 12.

PubMed [citation]

PMID:: 23403622
PMCID:: PMC3624940

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003791388.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with AP3B1-related conditions. A gross deletion of the genomic region encompassing the full coding sequence of the AP3B1 gene has been identified. Loss-of-function variants in AP3B1 are known to be pathogenic (PMID: 16507770, 23403622). The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes.

#	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: Sep 29, 2024

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