chr3-10142139-T-C

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PM1PM2PM5PP3_StrongPP5_Very_Strong

The NM_000551.4(VHL):ā€‹c.292T>Cā€‹(p.Tyr98His) variant causes a missense change. The variant allele was found at a frequency of 0.000000691 in 1,447,832 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (ā˜…ā˜…). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Y98C) has been classified as Likely pathogenic.

Frequency

Genomes: not found (cov: 33)
Exomes š‘“: 6.9e-7 ( 0 hom. )

Consequence

VHL
NM_000551.4 missense

Scores

12
4
3

Clinical Significance

Pathogenic criteria provided, multiple submitters, no conflicts P:15

Conservation

PhyloP100: 5.03
Variant links:
Genes affected
VHL (HGNC:12687): (von Hippel-Lindau tumor suppressor) This gene encodes a component of a ubiquitination complex. The encoded protein is involved in the ubiquitination and degradation of hypoxia-inducible-factor (HIF), which is a transcription factor that plays a central role in the regulation of gene expression by oxygen. In addition to oxygen-related gene expression, this protein plays a role in many other cellular processes including cilia formation, cytokine signaling, regulation of senescence, and formation of the extracellular matrix. Variants of this gene are associated with von Hippel-Lindau syndrome, pheochromocytoma, erythrocytosis, renal cell carcinoma, and cerebellar hemangioblastoma. [provided by RefSeq, Jun 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 18 ACMG points.

PM1
In a chain von Hippel-Lindau disease tumor suppressor (size 212) in uniprot entity VHL_HUMAN there are 96 pathogenic changes around while only 8 benign (92%) in NM_000551.4
PM2
Very rare variant in population databases, with high coverage;
PM5
Other missense variant is known to change same aminoacid residue: Variant chr3-10142140-A-G is described in Lovd as [Likely_pathogenic].
PP3
MetaRNN computational evidence supports a deleterious effect, 0.984
PP5
Variant 3-10142139-T-C is Pathogenic according to our data. Variant chr3-10142139-T-C is described in ClinVar as [Pathogenic]. Clinvar id is 2223.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-10142139-T-C is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
VHLNM_000551.4 linkc.292T>C p.Tyr98His missense_variant Exon 1 of 3 ENST00000256474.3 NP_000542.1 P40337-1A0A024R2F2
VHLNM_001354723.2 linkc.292T>C p.Tyr98His missense_variant Exon 1 of 3 NP_001341652.1
VHLNM_198156.3 linkc.292T>C p.Tyr98His missense_variant Exon 1 of 2 NP_937799.1 P40337-2A0A0S2Z4K1
VHLNR_176335.1 linkn.362T>C non_coding_transcript_exon_variant Exon 1 of 4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
VHLENST00000256474.3 linkc.292T>C p.Tyr98His missense_variant Exon 1 of 3 1 NM_000551.4 ENSP00000256474.3 P40337-1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD3 exomes
AF:
0.0000134
AC:
3
AN:
223372
Hom.:
0
AF XY:
0.0000240
AC XY:
3
AN XY:
124746
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000199
Gnomad OTH exome
AF:
0.000177
GnomAD4 exome
AF:
6.91e-7
AC:
1
AN:
1447832
Hom.:
0
Cov.:
32
AF XY:
0.00
AC XY:
0
AN XY:
720736
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
9.00e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
33

ClinVar

Significance: Pathogenic
Submissions summary: Pathogenic:15
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

Von Hippel-Lindau syndrome Pathogenic:8
Nov 01, 2001
OMIM
Significance: Pathogenic
Review Status: no assertion criteria provided
Collection Method: literature only

- -

Dec 03, 2019
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The p.Tyr98His variant in VHL has been reported in >25 individuals with Von Hippel-Lindau disease and segregated with disease in >50 affected individuals from several families, and is considered a founder variant in the Black Forest region in Germany (Bender 2001). It has also been identified in 2/100722 of European chromosomes by gnomAD (http://gnomad.broadinstitute.org). This variant has also been reported in ClinVar (Variation ID 2223). Computational prediction tools and conservation analyses suggest that this variant may impact the protein, though this information is not predictive enough to determine pathogenicity. In vitro functional studies support an impact on protein function (Hoffman 2001, Clifford 2001, Shmueli 2013). In summary, this variant meets criteria to be classified as pathogenic for autosomal dominant Von Hippel- Lindeau disease. ACMG/AMP Criteria applied: PS4, PP1_Strong, PM2, PS3_Supporting, PP3. -

Jan 31, 2023
Myriad Genetics, Inc.
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

This variant is considered pathogenic. This variant has been reported in multiple individuals with clinical features of gene-specific disease [PMID: 11483638, 7759077, 34416425, 32869749, 31538058]. Functional studies indicate this variant impacts protein function [PMID: 28052007, 19602254, 16261165, 23840444, 11331612]. This variant is expected to disrupt protein structure [internal Myriad data]. -

Jun 21, 2023
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

Variant summary: VHL c.292T>C (p.Tyr98His) results in a conservative amino acid change located in the VHL beta/alpha domain (IPR022772) of the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 1.3e-05 in 223464 control chromosomes in gnomAD. c.292T>C has been reported in the literature in multiple individuals affected with Von Hippel-Lindau Syndrome, has been shown to segregate with disease, and has been considered a founder mutation in Black Forest region of Germany (example: Brauch_1995). At least one publication reports experimental evidence evaluating an impact on protein function. One of the most pronounced variant effects results in impaired binding with HIF protein (example: Couve_2014). These data indicate that the variant is very likely to be associated with disease. The following publications have been ascertained in the context of this evaluation (PMID: 7759077, 25371412). Twelve submitters have cited clinical-significance assessments for this variant to ClinVar after 2014 and all submitters have classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -

Feb 26, 2016
Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia
Significance: Pathogenic
Review Status: no assertion criteria provided
Collection Method: clinical testing

- -

Apr 20, 2022
MGZ Medical Genetics Center
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Mar 31, 2020
Johns Hopkins Genomics, Johns Hopkins University
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

May 24, 2019
Clinical Genomics Labs, University Health Network
Significance: Pathogenic
Review Status: no assertion criteria provided
Collection Method: clinical testing

- -

not provided Pathogenic:4
Feb 15, 2019
Athena Diagnostics
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The best available variant frequency is uninformative because it is below the disease allele frequency. Found in at least one symptomatic patient. Predicted to have a damaging effect on the protein. Damaging to protein function(s) relevant to disease mechanism. Moderate co-segregation with disease. However, available data are from a single family. -

Feb 15, 2019
Quest Diagnostics Nichols Institute San Juan Capistrano
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

This variant has been reported as pathogenic in multiple individuals and families with Von Hippel-Lindau disease in the published literature, where it has been shown to segregate with disease (PMIDs: 21204227 (2011), 19763184 (2009), 19336503 (2009), 11709017 (2001), 11483638 (2001), 10567493 (1999), 10408776 (1999), and 7759077 (1995)). Multiple experimental studies indicate that the variant is damaging to VHL protein function (PMIDs: 28643803 (2017), 20855504 (2010), 20388653 (2010), 19620968 (2009), and 16261165 (2006)). Therefore, the variant is classified as pathogenic. -

Mar 23, 2015
Eurofins Ntd Llc (ga)
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Feb 01, 2022
CeGaT Center for Human Genetics Tuebingen
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

VHL-related disorder Pathogenic:1
Nov 22, 2023
PreventionGenetics, part of Exact Sciences
Significance: Pathogenic
Review Status: no assertion criteria provided
Collection Method: clinical testing

The VHL c.292T>C variant is predicted to result in the amino acid substitution p.Tyr98His. This variant has previously been reported in multiple individuals with pheochromocytoma and Von Hippel-Lindau disease (Crossey et al. 1994. PubMed ID: 7987306, described as 505T>C/169Tyr>His; Boedeker et al. 2009. PubMed ID: 19336503; Gallou et al. 1999. PubMed ID: 10408776; Nielsen et al. 2011. PubMed ID: 21204227). This variant is reported in 3 of ~233,000 alleles in gnomAD and is interpreted as pathogenic in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/103904398/). This variant is interpreted as pathogenic. -

Von Hippel-Lindau syndrome;C1837915:Chuvash polycythemia Pathogenic:1
May 21, 2024
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

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. -

Hereditary cancer-predisposing syndrome Pathogenic:1
Jun 17, 2024
Ambry Genetics
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The p.Y98H pathogenic mutation (also known as c.292T>C), located in coding exon 1 of the VHL gene, results from a T to C substitution at nucleotide position 292. The tyrosine at codon 98 is replaced by histidine, an amino acid with similar properties. This mutation has been reported in numerous VHL families in the literature (Crossey PA et al. Hum Mol Genet. 1994 Aug;3:1303-8; Neumann HP et al. N Engl J Med. 2002 May;346:1459-66; Gallou C et al. Hum. Mutat. 2004 Sep;24:215-24; Boedeker CC et al. J. Clin. Endocrinol. Metab. 2009 Jun;94:1938-44; Erlic Z et al. Endocr Relat Cancer. 2010 Dec;17:875-83; Nielsen SM et al. Am J Med Genet A. 2011 Jan;155A:168-73; Klingler JH et al. J Stroke Cerebrovasc Dis. 2013 May;22:437-43; Huang KL et al. Cell. 2018 04;173:355-370.e14; Liu P et al. Gland Surg, 2019 Aug;8:343-353). In addition, this mutation was shown to disrupt microtubule stabilization in vitro and has been noted to be associated with Type 2A VHL (Hergovich A et al. Nat Cell Biol. 2003;5(1):64-70; Bangiyeva V et al. BMC Cancer. 2009;9:229). Of note, this may be referred to as c.505T>A in some literature. Based on available evidence to date, this alteration is considered to be pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.97
BayesDel_addAF
Pathogenic
0.48
D
BayesDel_noAF
Pathogenic
0.48
CADD
Pathogenic
26
DANN
Uncertain
1.0
DEOGEN2
Pathogenic
0.99
D;.
Eigen
Pathogenic
0.72
Eigen_PC
Uncertain
0.66
FATHMM_MKL
Pathogenic
0.98
D
LIST_S2
Benign
0.84
T;T
M_CAP
Pathogenic
0.99
D
MetaRNN
Pathogenic
0.98
D;D
MetaSVM
Pathogenic
0.81
D
MutationAssessor
Uncertain
2.6
M;M
PrimateAI
Pathogenic
0.84
D
PROVEAN
Uncertain
-3.9
D;D
REVEL
Pathogenic
0.88
Sift
Benign
0.043
.;D
Sift4G
Pathogenic
0.0
D;T
Polyphen
1.0
D;D
Vest4
0.89
MutPred
0.86
Loss of glycosylation at P103 (P = 0.0211);Loss of glycosylation at P103 (P = 0.0211);
MVP
1.0
MPC
1.2
ClinPred
0.97
D
GERP RS
5.2
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.91
gMVP
0.99

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs5030809; hg19: chr3-10183823; API