NM_000551.4(VHL):c.416C>T (p.Ser139Phe) AND Hereditary cancer-predisposing syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 20, 2022
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:: RCV004020464.1

Allele description [Variation Report for NM_000551.4(VHL):c.416C>T (p.Ser139Phe)]

NM_000551.4(VHL):c.416C>T (p.Ser139Phe)

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.416C>T (p.Ser139Phe)

HGVS:

NC_000003.12:g.10146589C>T
NG_008212.3:g.9955C>T
NG_046756.1:g.4351C>T
NM_000551.4:c.416C>TMANE SELECT
NM_001354723.2:c.*18-3198C>T
NM_198156.3:c.341-3198C>T
NP_000542.1:p.Ser139Phe
NP_000542.1:p.Ser139Phe
LRG_322t1:c.416C>T
LRG_322:g.9955C>T
LRG_322p1:p.Ser139Phe
NC_000003.11:g.10188273C>T
NM_000551.3:c.416C>T

Protein change:

S139F

Links:

dbSNP: rs587780732

NCBI 1000 Genomes Browser:

rs587780732

Molecular consequence:

NM_001354723.2:c.*18-3198C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_198156.3:c.341-3198C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_000551.4:c.416C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Hereditary cancer-predisposing syndrome
Synonyms:: Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV005036463	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Sep 20, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV005036463

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Sep 20, 2022)

germline

clinical testing

Citation Link

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

Details of each submission

From Ambry Genetics, SCV005036463.1

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

Description

The p.S139F variant (also known as c.416C>T), located in coding exon 2 of the VHL gene, results from a C to T substitution at nucleotide position 416. The serine at codon 139 is replaced by phenylalanine, an amino acid with highly dissimilar properties. This amino acid position is not well conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

#	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: Nov 10, 2024

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