FKBP15

protein-coding

FKBP prolyl isomerase family member 15, the group of FKBP prolyl isomerases|Protein phosphatase 1 regulatory subunits

Gene summary

Predicted to enable actin binding activity and peptidyl-prolyl cis-trans isomerase activity. Predicted to be involved in endocytosis. Located in membrane. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

KIAA0674

MANE transcript

NM_015258.2

Inheritance

—

ClinVar variants

U:168B:11

Top phenotype

Inborn genetic diseases

gnomAD constraint

pLI —, LoF o/e 0.45

Max pathogenic AF

—

Genomic locus

chr9:113,161,006-113,221,458

External References & Databases

Ensembl (ENSG00000119321)

Transcript & Mutation Effects

hg38 • Region Span ~60.5 kb

Loading mutation effect viewer...

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 FKBP15 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 163

Inborn genetic diseasesTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015258.2. 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			4 clinvar	1 clinvar		5
missense			157 clinvar	10 clinvar		167
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			7 clinvar			7
Total	0	0	168	11	0	179

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 39 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_015258.2	RefSeq	NP_056073.1	28	MANE Select
ENST00000238256.8	Ensembl	ENSP00000238256.3	28	MANE Select
ENST00000414250.2	Ensembl	ENSP00000415733.2	14	Standard
ENST00000414250.3	Ensembl	ENSP00000415733.2	14	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

TYROBP Causal Network

Biological Process

endocytosis
negative regulation of phosphatase activity

Molecular Function

actin binding
protein binding

Cellular Component

early endosome
actin filament
membrane
growth cone

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000238256
Coding exons: 28
Length: 60356
Individuals with no LoFs: 124578
Homozygous LoFs: 0
Heterozygous LoFs: 76
Defined: 124654
p: 0.000305

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.58	536	649	0.825	0.0000338	7881
Missense (PolyPhen)		156	201.25	0.77517		2516
Synonymous	0.372	242	249	0.970	0.0000139	2362
Loss of Function	4.23	31	68.9	0.450	0.00000356	802

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00040	0.00039	rare
Latino/Admixed American	0.00018	0.00017	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00022	0.00022	rare
Finnish	0.00023	0.00023	rare
European (Non-Finnish)	0.00041	0.00040	rare
South Asian	0.00023	0.00023	rare
Other	0.00034	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be involved in the cytoskeletal organization of neuronal growth cones. Seems to be inactive as a PPIase (By similarity). Involved in the transport of early endosomes at the level of transition between microfilament-based and microtubule- based movement. {ECO:0000250, ECO:0000269|PubMed:19121306}.;

Recessive Scores

pRec: 0.0960

Intolerance Scores

LoFtool: 0.783
RVIS EVS: 0.21
RVIS percentile EVS: 67.54

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.0000834

Gene Damage Prediction

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