PFDN6

prefoldin subunit 6, the group of MicroRNA protein coding host genes|Prefoldin subunits

Basic information

Region (hg38): 6:33289302-33298401

Previous symbols: [ "HKE2" ]

Links

ENSG00000204220 ∙ NCBI:10471 ∙ OMIM:605660 ∙ HGNC:4926 ∙ Uniprot:O15212 ∙ 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 PFDN6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PFDN6 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					1	1
missense			3			3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	3	0	1

Variants in PFDN6

This is a list of pathogenic ClinVar variants found in the PFDN6 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-33290408-G-A		not specified	Uncertain significance (Feb 22, 2023)
6-33290435-A-G		not specified	Uncertain significance (Aug 20, 2024)
6-33290834-G-A		not specified	Uncertain significance (Apr 15, 2024)
6-33290842-C-A			Benign (Feb 25, 2018)
6-33292134-T-C		not specified	Uncertain significance (Dec 10, 2024)
6-33292157-C-A		not specified	Uncertain significance (May 23, 2023)
6-33292157-C-T		not specified	Uncertain significance (Nov 07, 2022)
6-33292196-G-A		not specified	Uncertain significance (Jun 25, 2024)
6-33292305-T-G		not specified	Uncertain significance (Jun 10, 2024)
6-33292463-A-G		not specified	Uncertain significance (May 02, 2024)
6-33292487-G-A		not specified	Uncertain significance (May 13, 2024)
6-33292504-A-G		not specified	Uncertain significance (Dec 21, 2023)
6-33292507-C-T		not specified	Uncertain significance (Oct 20, 2023)
6-33293041-T-C		not specified	Uncertain significance (Jan 20, 2023)
6-33293074-C-T		not specified	Uncertain significance (Aug 28, 2024)
6-33293126-C-T		not specified	Likely benign (Nov 16, 2021)
6-33293143-C-A		not specified	Uncertain significance (Jan 08, 2024)
6-33293189-G-C		not specified	Uncertain significance (May 23, 2024)
6-33293230-G-A		not specified	Uncertain significance (Nov 29, 2024)
6-33293257-C-G			Benign (Jan 19, 2018)
6-33293423-C-T		not specified	Uncertain significance (Nov 12, 2024)
6-33293424-G-A		not specified	Uncertain significance (Mar 31, 2024)
6-33293426-G-A		not specified	Uncertain significance (Jun 26, 2024)
6-33293462-C-G		not specified	Likely benign (May 03, 2023)
6-33293478-G-A		not specified	Uncertain significance (Jan 19, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PFDN6	protein_coding	protein_coding	ENST00000395131	4	9100

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.936	0.0638	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.41	36	68.8	0.523	0.00000366	813
Missense in Polyphen		3	18.62	0.16112		254
Synonymous	1.03	23	30.2	0.761	0.00000162	262
Loss of Function	2.74	0	8.73	0.00	4.58e-7	90

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)	0.00	0.00
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: 0.149

Intolerance Scores

• loftool: 0.545
• rvis_EVS: 0.32
• rvis_percentile_EVS: 72.94

Haploinsufficiency Scores

• pHI: 0.333
• hipred: Y
• hipred_score: 0.775
• ghis: 0.545

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.977

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pfdn6
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: protein folding;chaperone-mediated protein complex assembly
• Cellular component: cytoplasm;prefoldin complex
• Molecular function: unfolded protein binding;chaperone binding