NM_000551.4(VHL):c.292T>C (p.Tyr98His) AND multiple conditions

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jan 8, 2024
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:: RCV000684783.16

Allele description [Variation Report for NM_000551.4(VHL):c.292T>C (p.Tyr98His)]

NM_000551.4(VHL):c.292T>C (p.Tyr98His)

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.292T>C (p.Tyr98His)

HGVS:

NC_000003.12:g.10142139T>C
NG_008212.3:g.5505T>C
NM_000551.4:c.292T>CMANE SELECT
NM_001354723.2:c.292T>C
NM_198156.3:c.292T>C
NP_000542.1:p.Tyr98His
NP_000542.1:p.Tyr98His
NP_001341652.1:p.Tyr98His
NP_937799.1:p.Tyr98His
LRG_322t1:c.292T>C
LRG_322:g.5505T>C
LRG_322p1:p.Tyr98His
NC_000003.11:g.10183823T>C
NM_000551.2:c.292T>C
NM_000551.3:c.292T>C
P40337:p.Tyr98His
p.[Tyr98His]

Protein change:

Y98H; TYR98HIS

Links:

UniProtKB: P40337#VAR_005707; OMIM: 608537.0009; dbSNP: rs5030809

NCBI 1000 Genomes Browser:

rs5030809

Molecular consequence:

NM_000551.4:c.292T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001354723.2:c.292T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_198156.3:c.292T>C - missense variant - [Sequence Ontology: SO:0001583]

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

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000553393	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jan 8, 2024)	germline	clinical testing	PubMed (15) [See all records that cite these PMIDs] 7728151, 7759077, 10408776, 11483638, 19336503, 19763184, 21204227, 10878807, 11331612, 11331613, 12510195, 16261165, 23840444, 25371412, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000553393

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jan 8, 2024)

germline

clinical testing

PubMed (15)
[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

Germline mutations in the von Hippel-Lindau disease tumor suppressor gene: correlations with phenotype.

Chen F, Kishida T, Yao M, Hustad T, Glavac D, Dean M, Gnarra JR, Orcutt ML, Duh FM, Glenn G, et al.

Hum Mutat. 1995;5(1):66-75.

PubMed [citation]

PMID:: 7728151

Von Hippel-Lindau (VHL) disease with pheochromocytoma in the Black Forest region of Germany: evidence for a founder effect.

Brauch H, Kishida T, Glavac D, Chen F, Pausch F, Höfler H, Latif F, Lerman MI, Zbar B, Neumann HP.

Hum Genet. 1995 May;95(5):551-6.

PubMed [citation]

PMID:: 7759077

See all PubMed Citations (15)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000553393.9

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (15)

Description

This sequence change replaces tyrosine, which is neutral and polar, with histidine, which is basic and polar, at codon 98 of the VHL protein (p.Tyr98His). This variant is present in population databases (rs5030809, gnomAD 0.002%). This missense change has been observed in individual(s) with clinical features of VHL-related conditions (PMID: 7728151, 7759077, 10408776, 11483638, 19336503, 19763184, 21204227). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 2223). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt VHL protein function with a positive predictive value of 95%. Experimental studies have shown that this missense change affects VHL function (PMID: 10878807, 11331612, 11331613, 12510195, 16261165, 23840444, 25371412). 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 26, 2024

ClinVar

Relating variation to medicine