NM_000551.4(VHL):c.463+3A>G AND not provided

Germline classification:: Uncertain significance (3 submissions)
Last evaluated:: Apr 12, 2016
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:: RCV000587888.3

Allele description [Variation Report for NM_000551.4(VHL):c.463+3A>G]

NM_000551.4(VHL):c.463+3A>G

Genes:

LOC107303340:3p25 von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase Alu-mediated recombination region [Gene]
VHL:von Hippel-Lindau tumor suppressor [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

3p25.3

Genomic location:

Preferred name:

NM_000551.4(VHL):c.463+3A>G

HGVS:

NC_000003.12:g.10146639A>G
NG_008212.3:g.10005A>G
NG_046756.1:g.4401A>G
NM_000551.4:c.463+3A>GMANE SELECT
NM_001354723.2:c.*18-3148A>G
NM_198156.3:c.341-3148A>G
LRG_322t1:c.463+3A>G
LRG_322:g.10005A>G
NC_000003.11:g.10188323A>G
NM_000551.3:c.463+3A>G

Links:

dbSNP: rs1131690954

NCBI 1000 Genomes Browser:

rs1131690954

Molecular consequence:

NM_000551.4:c.463+3A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001354723.2:c.*18-3148A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_198156.3:c.341-3148A>G - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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PREDICTED: kin of IRRE-like protein 3, partial [Balearica regulorum gibbericeps]
PREDICTED: kin of IRRE-like protein 3, partial [Balearica regulorum gibbericeps]
gi|723574755|ref|XP_010307361.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000697516	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Uncertain significance (Apr 12, 2016)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 22145147, 24977658, 22438210 LabCorp Variant Classification Summary - May 2015.docx, Citation Link,
SCV001927631	Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Pathogenic	germline	clinical testing
SCV001973440	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Pathogenic	germline	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000697516

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Uncertain significance
(Apr 12, 2016)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

LabCorp Variant Classification Summary - May 2015.docx,

Citation Link,

SCV001927631

Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus

See additional submitters

no assertion criteria provided

Pathogenic

germline

clinical testing

SCV001973440

Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus

See additional submitters

no assertion criteria provided

Pathogenic

germline

clinical testing

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Role of cortical sparing adrenalectomy and novel variant of mutation in patient with von Hippel-Lindau disease.

Boaz RJ, Ramakant P, Ebenazer A, Pai R, Rajaratnam S, Abraham D, Paul MJ.

Indian J Endocrinol Metab. 2011 Oct;15 Suppl 4:S402-5. doi: 10.4103/2230-8210.86987.

PubMed [citation]

PMID:: 22145147
PMCID:: PMC3230085

Mutations seen among patients with pheochromocytoma and paraganglioma at a referral center from India.

Pai R, Ebenazer A, Paul MJ, Thomas N, Nair A, Seshadri MS, Oommen R, Shanthly N, Devasia A, Rebekah G, Jeyaseelan L, Rajaratnam S.

Horm Metab Res. 2015 Feb;47(2):133-7. doi: 10.1055/s-0034-1376989. Epub 2014 Jun 30.

PubMed [citation]

PMID:: 24977658

See all PubMed Citations (3)

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000697516.1

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

Description

Variant summary: The variant of interest is located at a conserved intronic position with 3/5 in silico programs via Alamut predicting an effect on splicing, although these predictions have yet to be functionally assessed. The variant of interest was not observed in controls (ExAC, 1000 Gs or ESP) and has been reported in affected individuals via publications. However, no reputable databases and/or clinical laboratories cite the variant. Although, another variant at this position, c.463+3A>T has been reported in affected individuals via publications. Therefore, taking all lines of evidence into consideration, the variant of interest is classified as VUS-possibly pathogenic until additional information becomes available.

#	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

From Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus, SCV001927631.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus, SCV001973440.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: May 1, 2024

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