PFDN4

prefoldin subunit 4, the group of Prefoldin subunits

Basic information

Region (hg38): 20:54207921-54228052

Links

ENSG00000101132 ∙ NCBI:5203 ∙ OMIM:604898 ∙ HGNC:8868 ∙ Uniprot:Q9NQP4 ∙ 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 PFDN4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PFDN4 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			6			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	0	0

Variants in PFDN4

This is a list of pathogenic ClinVar variants found in the PFDN4 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-54208114-T-C		not specified	Uncertain significance (Aug 28, 2023)
20-54214351-G-C		not specified	Uncertain significance (May 26, 2024)
20-54214367-A-G		not specified	Uncertain significance (Mar 19, 2024)
20-54214409-G-A		not specified	Uncertain significance (Aug 22, 2023)
20-54215339-A-C		not specified	Uncertain significance (May 18, 2023)
20-54215402-T-C		not specified	Uncertain significance (Jun 28, 2024)
20-54219028-C-A		not specified	Uncertain significance (Feb 06, 2024)
20-54219074-G-A		not specified	Uncertain significance (Aug 08, 2023)
20-54219082-G-A		not specified	Uncertain significance (Mar 22, 2023)
20-54219115-G-C		not specified	Uncertain significance (Oct 09, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PFDN4	protein_coding	protein_coding	ENST00000371419	4	20206

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.476	0.503	122426	0	1	122427	0.00000408

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.21	35	61.8	0.567	0.00000303	893
Missense in Polyphen		6	13.793	0.43501		239
Synonymous	-0.598	24	20.6	1.17	0.00000108	213
Loss of Function	1.85	1	5.81	0.172	2.43e-7	92

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000899	0.00000899
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

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}.
• Pathway: 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 (Consensus)

Recessive Scores

• pRec: 0.221

Intolerance Scores

• loftool: 0.406
• rvis_EVS: 0.3
• rvis_percentile_EVS: 71.81

Haploinsufficiency Scores

• pHI: 0.547
• hipred: Y
• hipred_score: 0.804

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.974

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pfdn4

Gene ontology

• Biological process: protein folding
• Cellular component: nucleus;cytoplasm;mitochondrion;cytosol;prefoldin complex
• Molecular function: protein binding;unfolded protein binding;chaperone binding