NM_000551.4(VHL):c.376G>C (p.Asp126His) AND multiple conditions

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Nov 7, 2018
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:: RCV000631278.8

Allele description [Variation Report for NM_000551.4(VHL):c.376G>C (p.Asp126His)]

NM_000551.4(VHL):c.376G>C (p.Asp126His)

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.376G>C (p.Asp126His)

HGVS:

NC_000003.12:g.10146549G>C
NG_008212.3:g.9915G>C
NG_046756.1:g.4311G>C
NM_000551.4:c.376G>CMANE SELECT
NM_001354723.2:c.*18-3238G>C
NM_198156.3:c.341-3238G>C
NP_000542.1:p.Asp126His
NP_000542.1:p.Asp126His
LRG_322t1:c.376G>C
LRG_322:g.9915G>C
LRG_322p1:p.Asp126His
NC_000003.11:g.10188233G>C
NM_000551.3:c.376G>C

Protein change:

D126H

Links:

dbSNP: rs104893831

NCBI 1000 Genomes Browser:

rs104893831

Molecular consequence:

NM_001354723.2:c.*18-3238G>C - intron variant - [Sequence Ontology: SO:0001627]
NM_198156.3:c.341-3238G>C - intron variant - [Sequence Ontology: SO:0001627]
NM_000551.4:c.376G>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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maturase K, partial (chloroplast) [Tachigali macrostachya]
maturase K, partial (chloroplast) [Tachigali macrostachya]
gi|960527554|gb|ALR87447.1|

Protein
maturase K, partial (chloroplast) [Tachigali hypoleuca]
maturase K, partial (chloroplast) [Tachigali hypoleuca]
gi|960527550|gb|ALR87445.1|

Protein
SPTP3101_p54 [Staphylococcus phage tp310-1]
SPTP3101_p54 [Staphylococcus phage tp310-1]
Gene ID:5525350

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000752306	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Nov 7, 2018)	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

SCV000752306

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Nov 7, 2018)

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, SCV000752306.5

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

Description

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. Algorithms developed to predict the effect of missense changes on protein structure and function do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). This variant has not been reported in the literature in individuals with VHL-related disease. This variant is not present in population databases (ExAC no frequency). This sequence change replaces aspartic acid with histidine at codon 126 of the VHL protein (p.Asp126His). The aspartic acid residue is moderately conserved and there is a moderate physicochemical difference between aspartic acid and histidine.

#	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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