VBP1

protein-coding

VHL binding protein 1, the group of Prefoldin subunits

Gene summary

The protein encoded by this gene interacts with the Von Hippel-Lindau protein to form an intracellular complex. The encoded protein functions as a chaperone protein, and may play a role in the transport of the Von Hippel-Lindau protein from the perinuclear granules to the nucleus or cytoplasm. Alternative splicing and the use of alternate transcription start sites results in multiple transcript variants encoding different protein isoforms. [provided by RefSeq, Jan 2015]

MANE transcript

NM_003372.7

Inheritance

—

ClinVar variants

U:39B:2

Top phenotype

Ependymoma

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chrX:155,197,007-155,239,841

External References & Databases

Ensembl (ENSG00000155959)

Transcript & Mutation Effects

hg38 • Region Span ~42.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to VBP1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 8

not providedTotal: 2

EpendymomaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_003372.7. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			5 clinvar	1 clinvar	1 clinvar	7
missense			22 clinvar			22
nonsense			3 clinvar			3
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			9 clinvar			9
Total	0	0	39	1	1	41

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 19 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_003372.7	RefSeq	NP_003363.1	6	MANE Select
ENST00000286428.7	Ensembl	ENSP00000286428.5	6	MANE Select
NM_001303543.1	RefSeq	NP_001290472.1	6	Standard
NM_001303544.1	RefSeq	NP_001290473.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Metabolism of proteins
Chaperonin-mediated protein folding
Protein folding
Prefoldin mediated transfer of substrate to CCT/TriC
Cooperation of Prefoldin and TriC/CCT in actin and tubulin folding

Biological Process

protein folding
microtubule-based process
tubulin complex assembly

Molecular Function

protein binding
tubulin binding

Cellular Component

nucleus
cytoplasm
cytosol
polysome
prefoldin complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000286428
Coding exons: 6
Length: 42815
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.36	32	62.1	0.515	0.00000407	1302
Missense (PolyPhen)		6	19.331	0.31039		436
Synonymous	-0.766	28	23.3	1.20	0.00000163	338
Loss of Function	2.46	0	7.02	0.00	4.98e-7	140

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Binds specifically to cytosolic chaperonin (c-CPN) and transfers target proteins to it. Binds to nascent polypeptide chain and promotes folding in an environment in which there are many competing pathways for nonnative proteins. {ECO:0000269|PubMed:9630229}.;

Recessive Scores

pRec: 0.129

Intolerance Scores

RVIS EVS: -0.01
RVIS percentile EVS: 52.85

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.781

Gene Damage Prediction

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