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NM_000551.4(VHL):c.340+770T>C AND Chuvash polycythemia

Germline classification:
Pathogenic (2 submissions)
Last evaluated:
Feb 23, 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:
RCV001007626.4

Allele description [Variation Report for NM_000551.4(VHL):c.340+770T>C]

NM_000551.4(VHL):c.340+770T>C

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.340+770T>C
HGVS:
  • NC_000003.12:g.10142957T>C
  • NG_008212.3:g.6323T>C
  • NG_046756.1:g.719T>C
  • NM_000551.4:c.340+770T>CMANE SELECT
  • NM_001354723.2:c.535T>C
  • NM_198156.3:c.340+770T>C
  • NP_001341652.1:p.Ser179Pro
  • LRG_322t1:c.340+770T>C
  • LRG_322:g.6323T>C
  • NC_000003.11:g.10184641T>C
  • NM_000551.3:c.340+770T>C
  • c.340+770T-C
Protein change:
S179P
Links:
OMIM: 608537.0030; dbSNP: rs1346312258
NCBI 1000 Genomes Browser:
rs1346312258
Molecular consequence:
  • NM_000551.4:c.340+770T>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_198156.3:c.340+770T>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354723.2:c.535T>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

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001167314OMIM
no assertion criteria provided
Pathogenic
(Jan 1, 2005)
germlineliterature only

PubMed (2)
[See all records that cite these PMIDs]

SCV004813671Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)
Pathogenic
(Feb 23, 2024)
germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Mutations in the von Hippel-Lindau (VHL) tumor suppressor gene and VHL-haplotype analysis in patients with presumable congenital erythrocytosis.

Cario H, Schwarz K, Jorch N, Kyank U, Petrides PE, Schneider DT, Uhle R, Debatin KM, Kohne E.

Haematologica. 2005 Jan;90(1):19-24.

PubMed [citation]
PMID:
15642664

Identification of a new VHL exon and complex splicing alterations in familial erythrocytosis or von Hippel-Lindau disease.

Lenglet M, Robriquet F, Schwarz K, Camps C, Couturier A, Hoogewijs D, Buffet A, Knight SJL, Gad S, Couvé S, Chesnel F, Pacault M, Lindenbaum P, Job S, Dumont S, Besnard T, Cornec M, Dreau H, Pentony M, Kvikstad E, Deveaux S, Burnichon N, et al.

Blood. 2018 Aug 2;132(5):469-483. doi: 10.1182/blood-2018-03-838235. Epub 2018 Jun 11.

PubMed [citation]
PMID:
29891534
See all PubMed Citations (3)

Details of each submission

From OMIM, SCV001167314.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (2)

Description

In 4 patients from 3 unrelated families (F1, F2, and F3) with familial erythrocytosis-2 (ECYT2; 263400), Lenglet et al. (2018) identified compound heterozygous mutations in the VHL gene. All 4 patients carried a T-to-C transition (c.340+770T-C) in cryptic exon 1-prime (E1-prime), resulting in a splicing alteration, on 1 allele. Three patients from F2 and F3 had previously been diagnosed with Chuvash polycythemia since they were heterozygous for the R200W mutation (608537.0019) on the other allele. Prior to the study of Lenglet et al. (2018), these patients were thought to carry only 1 VHL mutation (the patient from F2 had previously been reported by Cario et al., 2005). The mutations, which were found by a combination of whole-genome and Sanger sequencing, segregated with the disorder in the families. RT-PCR analysis of lymphoblastoid cells from 1 patient (F1) showed a decrease in the exon 1/exon 2/exon 3 isoform and an increase in an exon 1/exon 3 isoform compared to wildtype. The patient from F1 carried a synonymous c.429C-T transition (asp143-to-asp, D143D) on the other allele, which also affected splicing. Two further unrelated patients with ECYT2 (families F9 and F10) were homozygous for the c.429C-T transition in the VHL gene. RT-PCR analysis from lymphocytes derived from these patients showed decreased mRNA levels, increased amounts of the E1/E3 transcripts, and severe decreases in the wildtype VHL mRNA and protein isoform compared to controls, suggesting that the mutation resulted in the skipping of exon 2. The 2 patients from families F9 and F10 also had mutations in the HBB gene (141900), which may have compensated for the ECYT2.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot providednot providednot providednot provided

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV004813671.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

Variant summary: VHL c.340+770T>C is located at a position not widely known to affect splicing. Consensus agreement among computation tools predict no significant impact on normal splicing. However, functional studies have shown that the variant leads to increased expression of minor, alternate mRNA isoforms containing a cryptic exon (termed E1', which is found deep in intron 1 and contains a premature stop codon) while simultaneously resulting in a strong decrease of predominant mRNA isoforms, which was associated with a downregulation of VHL protein expression (Lenglet_2018). The variant allele was found at a frequency of 1.3e-05 in 152334 control chromosomes (gnomAD v4). c.340+770T>C has been reported in the literature in multiple homozygous- and compound heterozygous individuals affected with autosomal recessive Congenital Polycythemia also referred to as familial erythrocytosis type 2 or Chuvash polycythemia (e.g. Lenglet_2018, Sochorcova_2023). In the heterozygous state, the variant is not expected to cause Von Hippel-Lindau Syndrome, as the heterozygous family members (carriers) were reportedly unaffected in these studies. The following publications have been ascertained in the context of this evaluation (PMID: 29891534, 37246471). ClinVar contains an entry for this variant (Variation ID: 816685). Based on the evidence outlined above, the variant was classified as pathogenic for Congenital Polycythemia.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Jul 23, 2024