VHLL

VHL like

Basic information

Region (hg38): 1:156298624-156299307

Previous symbols: [ "VHLP" ]

Links

ENSG00000189030 ∙ NCBI:391104 ∙ OMIM:619650 ∙ HGNC:30666 ∙ Uniprot:Q6RSH7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the VHLL gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VHLL gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			10			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	0	0

Variants in VHLL

This is a list of pathogenic ClinVar variants found in the VHLL region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-156298822-T-C		not specified	Uncertain significance (Jun 22, 2021)
1-156298834-A-G		not specified	Uncertain significance (Feb 22, 2023)
1-156298886-T-C		not specified	Uncertain significance (Jul 20, 2021)
1-156298994-C-T		not specified	Uncertain significance (Apr 08, 2022)
1-156299039-G-C		not specified	Uncertain significance (Jan 07, 2022)
1-156299041-G-A		not specified	Uncertain significance (Aug 30, 2021)
1-156299042-A-G		not specified	Uncertain significance (Aug 30, 2021)
1-156299095-G-A		not specified	Uncertain significance (Feb 12, 2024)
1-156299120-C-T		not specified	Uncertain significance (Jul 09, 2021)
1-156299169-G-C		not specified	Uncertain significance (Mar 18, 2024)
1-156299176-G-A		not specified	Uncertain significance (Apr 15, 2024)
1-156299179-C-G		not specified	Uncertain significance (Apr 29, 2024)
1-156299179-C-T		not specified	Uncertain significance (Feb 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VHLL	protein_coding	protein_coding	ENST00000339922	1	1014

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.431	74	85.2	0.869	0.00000516	890
Missense in Polyphen		22	26.906	0.81768		290
Synonymous	0.412	34	37.2	0.914	0.00000230	297
Loss of Function

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish
East Asian
Finnish
European (Non-Finnish)
Middle Eastern
South Asian
Other

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Functions as a dominant-negative VHL to serve as a protector of HIFalpha. {ECO:0000269|PubMed:14757845}.

Haploinsufficiency Scores

• pHI: 0.105
• hipred: N
• hipred_score: 0.112
• ghis: 0.429

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Gene ontology

• Biological process: protein ubiquitination
• Cellular component: nucleus;VCB complex
• Molecular function: protein binding;ubiquitin protein ligase activity