FKBP9

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

Basic information

Region (hg38): 7:32957403-33006930

Links

ENSG00000122642 ∙ NCBI:11328 ∙ OMIM:616257 ∙ HGNC:3725 ∙ Uniprot:O95302 ∙ 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 FKBP9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FKBP9 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			27			27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	27	0	0

Variants in FKBP9

This is a list of pathogenic ClinVar variants found in the FKBP9 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-32957602-C-A		not specified	Uncertain significance (Sep 28, 2022)
7-32957715-C-A		not specified	Uncertain significance (Sep 29, 2023)
7-32957785-T-G		not specified	Uncertain significance (Dec 02, 2021)
7-32974691-T-A		not specified	Uncertain significance (Jun 19, 2024)
7-32974720-G-A		not specified	Uncertain significance (May 16, 2024)
7-32975241-A-G		not specified	Uncertain significance (Jul 30, 2023)
7-32975261-G-C		not specified	Uncertain significance (Jan 23, 2024)
7-32975262-A-G		not specified	Uncertain significance (May 28, 2024)
7-32975268-A-G		not specified	Uncertain significance (Sep 22, 2022)
7-32976380-C-T		not specified	Uncertain significance (Jan 26, 2022)
7-32976421-G-A		not specified	Uncertain significance (Mar 01, 2023)
7-32976447-G-C		not specified	Uncertain significance (Nov 01, 2021)
7-32976455-T-A		not specified	Uncertain significance (Feb 15, 2023)
7-32980378-G-A		not specified	Uncertain significance (Jul 12, 2022)
7-32980378-G-C		not specified	Uncertain significance (Mar 23, 2023)
7-32980457-T-C		not specified	Uncertain significance (Feb 17, 2024)
7-32980508-A-G		not specified	Uncertain significance (Jan 16, 2024)
7-32988521-G-A		not specified	Uncertain significance (May 30, 2024)
7-32988524-C-T		not specified	Uncertain significance (May 27, 2022)
7-32988559-C-T		not specified	Uncertain significance (Dec 07, 2023)
7-32996203-T-G		not specified	Uncertain significance (Mar 14, 2023)
7-32996247-C-A		not specified	Uncertain significance (May 26, 2023)
7-32996262-C-G		not specified	Uncertain significance (Mar 31, 2022)
7-32996319-C-T		not specified	Uncertain significance (Dec 27, 2022)
7-33000213-G-A		not specified	Uncertain significance (Mar 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FKBP9	protein_coding	protein_coding	ENST00000242209	10	49527

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000106	0.988	125711	0	36	125747	0.000143

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.16	265	323	0.819	0.0000180	3709
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000207	0.000207
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000177	0.000176
Middle Eastern	0.000109	0.000109
South Asian	0.000231	0.000229
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: PPIases accelerate the folding of proteins during protein synthesis.
• Pathway: Metabolism of proteins;Chaperonin-mediated protein folding;Association of TriC/CCT with target proteins during biosynthesis;Protein folding (Consensus)

Recessive Scores

• pRec: 0.111

Intolerance Scores

• loftool: 0.403
• rvis_EVS: 0.13
• rvis_percentile_EVS: 63.36

Haploinsufficiency Scores

• pHI: 0.476
• hipred: Y
• hipred_score: 0.563
• ghis: 0.538

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.236

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fkbp9
• Phenotype: homeostasis/metabolism phenotype

Gene ontology

• Biological process: protein peptidyl-prolyl isomerization;protein folding
• Cellular component: endoplasmic reticulum
• Molecular function: peptidyl-prolyl cis-trans isomerase activity;calcium ion binding