FKBP2

FKBP prolyl isomerase 2, the group of FKBP prolyl isomerases

Basic information

Region (hg38): 11:64241003-64244132

Links

ENSG00000173486 ∙ NCBI:2286 ∙ OMIM:186946 ∙ HGNC:3718 ∙ Uniprot:P26885 ∙ 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 FKBP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FKBP2 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			4			4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	4	1	0

Variants in FKBP2

This is a list of pathogenic ClinVar variants found in the FKBP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-64241552-G-A			Likely benign (Oct 01, 2022)
11-64242502-G-A		not specified	Uncertain significance (Oct 24, 2024)
11-64242509-A-G		not specified	Uncertain significance (Jan 21, 2025)
11-64242538-G-A		not specified	Uncertain significance (Dec 14, 2023)
11-64242547-A-G		not specified	Uncertain significance (Jul 14, 2021)
11-64243265-C-T		not specified	Uncertain significance (Feb 22, 2025)
11-64243285-C-G		not specified	Uncertain significance (Mar 13, 2023)
11-64244016-G-A		not specified	Uncertain significance (Feb 02, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FKBP2	protein_coding	protein_coding	ENST00000394540	5	3130

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0493	0.867	125721	0	8	125729	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.986	53	77.4	0.685	0.00000418	891
Missense in Polyphen		17	32.138	0.52896		387
Synonymous	0.352	30	32.6	0.922	0.00000169	289
Loss of Function	1.43	3	7.11	0.422	3.02e-7	84

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000153	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000269	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides.
• Pathway: Human Complement System (Consensus)

Recessive Scores

• pRec: 0.157

Intolerance Scores

• rvis_EVS: 0.06
• rvis_percentile_EVS: 58.26

Haploinsufficiency Scores

• pHI: 0.192
• hipred: Y
• hipred_score: 0.557
• ghis: 0.512

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.958

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fkbp2

Gene ontology

• Biological process: protein peptidyl-prolyl isomerization
• Cellular component: endoplasmic reticulum;endoplasmic reticulum membrane
• Molecular function: peptidyl-prolyl cis-trans isomerase activity;protein binding;FK506 binding