FKBP15

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

Basic information

Region (hg38): 9:113161005-113221458

Previous symbols: [ "KIAA0674" ]

Links

ENSG00000119321 ∙ NCBI:23307 ∙ OMIM:617398 ∙ HGNC:23397 ∙ Uniprot:Q5T1M5 ∙ 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 FKBP15 gene.

• Inborn genetic diseases (46 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FKBP15 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			43	2		45
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	44	2	0

Variants in FKBP15

This is a list of pathogenic ClinVar variants found in the FKBP15 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-113161590-A-G		not specified	Uncertain significance (Mar 29, 2023)
9-113166101-C-T		not specified	Uncertain significance (Oct 17, 2023)
9-113166130-G-A		not specified	Uncertain significance (Mar 02, 2023)
9-113166143-G-A		not specified	Uncertain significance (Dec 19, 2023)
9-113168536-T-C		not specified	Uncertain significance (Nov 18, 2022)
9-113169269-A-G		not specified	Likely benign (Sep 29, 2023)
9-113169290-C-T		not specified	Uncertain significance (May 22, 2023)
9-113169317-G-C		not specified	Uncertain significance (Apr 18, 2023)
9-113169323-G-A		not specified	Uncertain significance (Mar 24, 2023)
9-113169344-T-G		not specified	Uncertain significance (Jan 31, 2023)
9-113169393-C-T		not specified	Uncertain significance (Apr 07, 2023)
9-113169395-C-G		not specified	Uncertain significance (Nov 07, 2022)
9-113169398-T-C		not specified	Uncertain significance (Nov 07, 2022)
9-113169452-T-C		not specified	Uncertain significance (May 18, 2022)
9-113169485-G-A		not specified	Likely benign (Oct 12, 2021)
9-113169510-T-C		not specified	Likely benign (Dec 11, 2023)
9-113169567-G-A		not specified	Uncertain significance (Feb 03, 2022)
9-113169699-C-T		not specified	Uncertain significance (Dec 16, 2022)
9-113169711-T-C		not specified	Uncertain significance (Nov 07, 2022)
9-113169728-A-C		not specified	Uncertain significance (Apr 19, 2023)
9-113169773-G-A		not specified	Uncertain significance (Aug 04, 2022)
9-113169809-T-C		not specified	Uncertain significance (Feb 15, 2023)
9-113169892-G-T		not specified	Uncertain significance (Sep 26, 2023)
9-113170581-C-T		not specified	Uncertain significance (Feb 27, 2023)
9-113171586-C-T		not specified	Uncertain significance (Aug 17, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FKBP15	protein_coding	protein_coding	ENST00000238256	28	60356

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.55e-12	1.00	124578	0	76	124654	0.000305

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.58	536	649	0.825	0.0000338	7881
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000582	0.000568
Ashkenazi Jewish	0.0000994	0.0000994
East Asian	0.000225	0.000223
Finnish	0.000234	0.000232
European (Non-Finnish)	0.000409	0.000398
Middle Eastern	0.000225	0.000223
South Asian	0.000231	0.000229
Other	0.000338	0.000330

dbNSFP

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}.
• Pathway: TYROBP Causal Network (Consensus)

Recessive Scores

• pRec: 0.0960

Intolerance Scores

• loftool: 0.783
• rvis_EVS: 0.21
• rvis_percentile_EVS: 67.54

Haploinsufficiency Scores

• pHI: 0.624
• hipred: N
• hipred_score: 0.328
• ghis: 0.534

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0000834

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fkbp15

Gene ontology

• Biological process: endocytosis;negative regulation of phosphatase activity
• Cellular component: early endosome;actin filament;membrane;growth cone
• Molecular function: actin binding;protein binding