FKBP9

protein-coding

FKBP prolyl isomerase 9, the group of FKBP prolyl isomerases|EF-hand domain containing

Gene summary

Predicted to enable calcium ion binding activity and peptidyl-prolyl cis-trans isomerase activity. Predicted to be involved in protein folding. Predicted to be active in endoplasmic reticulum. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_007270.5

Inheritance

—

ClinVar variants

U:92B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.5

Max pathogenic AF

—

Genomic locus

chr7:32,957,404-33,006,930

External References & Databases

Ensembl (ENSG00000122642)

Transcript & Mutation Effects

hg38 • Region Span ~49.5 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 FKBP9 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 85

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_007270.5. 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			2 clinvar			2
missense			89 clinvar	1 clinvar		90
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	92	1	0	93

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 33 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_007270.5	RefSeq	NP_009201.2	10	MANE Select
ENST00000242209.9	Ensembl	ENSP00000242209.4	10	MANE Select
NM_001284341.2	RefSeq	NP_001271270.1	11	Standard
NM_001284343.2	RefSeq	NP_001271272.1	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Metabolism of proteins
Chaperonin-mediated protein folding
Association of TriC/CCT with target proteins during biosynthesis
Protein folding

Biological Process

protein peptidyl-prolyl isomerization
protein folding

Molecular Function

peptidyl-prolyl cis-trans isomerase activity
calcium ion binding

Cellular Component

endoplasmic reticulum

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000242209
Coding exons: 10
Length: 49527
Individuals with no LoFs: 125711
Homozygous LoFs: 0
Heterozygous LoFs: 36
Defined: 125747
p: 0.000143

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.16	265	323	0.819	0.0000180	3709
Missense (PolyPhen)		109	151.44	0.71975		1582
Synonymous	0.591	127	136	0.935	0.00000844	1135
Loss of Function	2.25	12	23.9	0.503	0.00000118	285

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.00014	0.00014	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00018	0.00018	rare
South Asian	0.00023	0.00023	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: PPIases accelerate the folding of proteins during protein synthesis.;

Recessive Scores

pRec: 0.111

Intolerance Scores

LoFtool: 0.403
RVIS EVS: 0.13
RVIS percentile EVS: 63.36

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.236

Gene Damage Prediction

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