NM_000551.4(VHL):c.55G>C (p.Gly19Arg) AND multiple conditions

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 25, 2021
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:: RCV001966298.6

Allele description [Variation Report for NM_000551.4(VHL):c.55G>C (p.Gly19Arg)]

NM_000551.4(VHL):c.55G>C (p.Gly19Arg)

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.55G>C (p.Gly19Arg)

HGVS:

NC_000003.12:g.10141902G>C
NG_008212.3:g.5268G>C
NM_000551.4:c.55G>CMANE SELECT
NM_001354723.2:c.55G>C
NM_198156.3:c.55G>C
NP_000542.1:p.Gly19Arg
NP_001341652.1:p.Gly19Arg
NP_937799.1:p.Gly19Arg
LRG_322:g.5268G>C
NC_000003.11:g.10183586G>C

Protein change:

G19R

Links:

dbSNP: rs1382387188

NCBI 1000 Genomes Browser:

rs1382387188

Molecular consequence:

NM_000551.4:c.55G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001354723.2:c.55G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_198156.3:c.55G>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

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Vitamin K1-d7 (0)
Conserved Domains
Golli-Mbp isoform X7 [Rattus norvegicus]
Golli-Mbp isoform X7 [Rattus norvegicus]
gi|2678909709|ref|XP_063133162.1|

Protein
Aphyonus gelatinosus recombination activating protein 1 (RAG1) gene, partial cds
Aphyonus gelatinosus recombination activating protein 1 (RAG1) gene, partial cds
gi|1026260911|gb|KX150877.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002248717	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jan 25, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002248717

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jan 25, 2021)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

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

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002248717.3

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

Description

This variant has not been reported in the literature in individuals with VHL-related conditions. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate insufficient coverage at this position in the ExAC database. This sequence change replaces glycine with arginine at codon 19 of the VHL protein (p.Gly19Arg). The glycine residue is weakly conserved and there is a moderate physicochemical difference between glycine and arginine. 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 not expected to disrupt VHL protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	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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