FKBP3

FKBP prolyl isomerase 3, the group of FKBP prolyl isomerases

Basic information

Region (hg38): 14:45115599-45135319

Links

ENSG00000100442 ∙ NCBI:2287 ∙ OMIM:186947 ∙ HGNC:3719 ∙ Uniprot:Q00688 ∙ 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 FKBP3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FKBP3 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			16	1		17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	1	0

Variants in FKBP3

This is a list of pathogenic ClinVar variants found in the FKBP3 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-45116223-T-G		not specified	Uncertain significance (Sep 09, 2024)
14-45116234-T-G		not specified	Uncertain significance (May 21, 2024)
14-45118082-C-T		not specified	Uncertain significance (Aug 04, 2023)
14-45118089-T-C		not specified	Uncertain significance (Dec 13, 2023)
14-45120895-T-A		not specified	Uncertain significance (Jan 26, 2023)
14-45120898-C-A		not specified	Uncertain significance (Jul 02, 2024)
14-45121545-G-A		not specified	Uncertain significance (Dec 03, 2021)
14-45129806-C-G		not specified	Uncertain significance (Mar 15, 2024)
14-45129844-G-A		not specified	Uncertain significance (May 18, 2022)
14-45129867-G-A		not specified	Uncertain significance (Feb 16, 2023)
14-45129880-T-C		not specified	Likely benign (Jul 06, 2021)
14-45129892-C-G		not specified	Uncertain significance (Jan 04, 2024)
14-45130715-T-C		not specified	Uncertain significance (Oct 04, 2022)
14-45130739-T-C		not specified	Uncertain significance (Aug 05, 2024)
14-45130770-T-C		not specified	Uncertain significance (Oct 01, 2024)
14-45134384-T-C		not specified	Uncertain significance (Mar 16, 2022)
14-45134435-G-A		not specified	Uncertain significance (Oct 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FKBP3	protein_coding	protein_coding	ENST00000216330	7	19720

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000660	0.920	125731	0	16	125747	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0162	114	114	1.00	0.00000524	1469
Missense in Polyphen		19	21.256	0.89388		314
Synonymous	-0.262	43	40.9	1.05	0.00000198	405
Loss of Function	1.55	7	13.1	0.536	6.17e-7	165

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000278	0.000275
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000468	0.0000462
European (Non-Finnish)	0.0000366	0.0000352
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000981	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: FK506- and rapamycin-binding proteins (FKBPs) constitute a family of receptors for the two immunosuppressants which inhibit T-cell proliferation by arresting two distinct cytoplasmic signal transmission pathways. PPIases accelerate the folding of proteins.
• Pathway: Signaling events mediated by HDAC Class I (Consensus)

Recessive Scores

• pRec: 0.139

Intolerance Scores

• loftool: 0.323
• rvis_EVS: -0.23
• rvis_percentile_EVS: 36.86

Haploinsufficiency Scores

• pHI: 0.607
• hipred: Y
• hipred_score: 0.816
• ghis: 0.681

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• gene_indispensability_pred: E
• gene_indispensability_score: 0.881

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fkbp3
• Phenotype: hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: protein peptidyl-prolyl isomerization
• Cellular component: nucleus
• Molecular function: RNA binding;peptidyl-prolyl cis-trans isomerase activity;protein binding;FK506 binding;signaling receptor activity