NC_000003.12:g.(?_10064723)_(10149971_?)del AND multiple conditions

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Dec 15, 2017
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:: RCV000558078.2

Allele description [Variation Report for NC_000003.12:g.(?_10064723)_(10149971_?)del]

NC_000003.12:g.(?_10064723)_(10149971_?)del

Genes:

LOC107303339:3p25 BRK1 Alu-mediated recombination region [Gene]
LOC107303338:3p25 FANCD2 Alu-mediated recombination region [Gene]
LOC107303340:3p25 von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase Alu-mediated recombination region [Gene]
LOC129936148:ATAC-STARR-seq lymphoblastoid active region 19416 [Gene]
LOC129936149:ATAC-STARR-seq lymphoblastoid active region 19417 [Gene]
BRK1:BRICK1 subunit of SCAR/WAVE actin nucleating complex [Gene - OMIM - HGNC]
FANCD2:FA complementation group D2 [Gene - OMIM - HGNC]
FANCD2OS:FANCD2 opposite strand [Gene - HGNC]
VHL:von Hippel-Lindau tumor suppressor [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

3p25.3

Genomic location:

Chr3: 10064723 - 10149971 (on Assembly GRCh38)

Preferred name:

NC_000003.12:g.(?_10064723)_(10149971_?)del

HGVS:

NC_000003.12:g.(?_10064723)_(10149971_?)del

Condition(s)

Name:: Chuvash polycythemia
Synonyms:: POLYCYTHEMIA, VHL-DEPENDENT; Erythrocytosis, familial, 2
Identifiers:: MONDO: MONDO:0009892; MedGen: C1837915; Orphanet: 238557; OMIM: 263400

Name:: Von Hippel-Lindau syndrome (VHLS)
Synonyms:: VHL syndrome; Von Hippel-Lindau
Identifiers:: MONDO: MONDO:0008667; MedGen: C0019562; Orphanet: 892; OMIM: 193300

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000626868	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Dec 15, 2017)	germline	clinical testing	PubMed (6) [See all records that cite these PMIDs] 20567917, 17537157, 8634692, 10830910, 10567493, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000626868

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Dec 15, 2017)

germline

clinical testing

PubMed (6)
[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

Clinical and molecular characterization of Brazilian families with von Hippel-Lindau disease: a need for delineating genotype-phenotype correlation.

Gomy I, Molfetta GA, de Andrade Barreto E, Ferreira CA, Zanette DL, Casali-da-Rocha JC, Silva WA Jr.

Fam Cancer. 2010 Dec;9(4):635-42. doi: 10.1007/s10689-010-9357-2.

PubMed [citation]

PMID:: 20567917

Associations between VHL genotype and clinical phenotype in familial von Hippel-Lindau disease.

Huang JS, Huang CJ, Chen SK, Chien CC, Chen CW, Lin CM.

Eur J Clin Invest. 2007 Jun;37(6):492-500.

PubMed [citation]

PMID:: 17537157

See all PubMed Citations (6)

Details of each submission

From Invitae, SCV000626868.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (6)

Description

A gross deletion of the genomic region encompassing the full coding sequence of the VHL gene has been identified. The boundaries of this event are unknown as the deletion extends beyond the assayed region for this gene and therefore may encompass additional genes. Deletions of the entire VHL gene have been reported in multiple individuals and families with von Hippel-Lindau syndrome (PMID: 10830910, 10567493, 8634692, 17537157, 20567917). Loss-of-function variants in VHL are known to be pathogenic (PMID: 8956040, 12202531). For these reasons, this variant has been classified as Pathogenic.

#	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: Oct 14, 2023

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