FNIP2

folliculin interacting protein 2, the group of DENN domain containing

Basic information

Region (hg38): 4:158769026-158908050

Links

ENSG00000052795 ∙ NCBI:57600 ∙ OMIM:612768 ∙ HGNC:29280 ∙ Uniprot:Q9P278 ∙ 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 FNIP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FNIP2 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				2	1	3
missense			51	8	1	60
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	51	10	2

Variants in FNIP2

This is a list of pathogenic ClinVar variants found in the FNIP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-158769237-C-G		not specified	Uncertain significance (Dec 10, 2024)
4-158769276-G-A		not specified	Uncertain significance (Oct 04, 2024)
4-158769277-C-T		not specified	Uncertain significance (Jun 12, 2023)
4-158825920-T-C		not specified	Uncertain significance (Jul 14, 2021)
4-158825942-A-G		not specified	Uncertain significance (Jul 27, 2024)
4-158825988-A-T		not specified	Uncertain significance (Sep 05, 2024)
4-158829131-G-A		not specified	Uncertain significance (Jun 03, 2024)
4-158831874-C-T		not specified	Uncertain significance (Jan 19, 2024)
4-158833607-T-C		not specified	Uncertain significance (Apr 25, 2022)
4-158851378-C-G		not specified	Uncertain significance (Jun 07, 2023)
4-158859090-A-T		not specified	Uncertain significance (Oct 06, 2021)
4-158859136-A-G		not specified	Uncertain significance (Apr 06, 2024)
4-158859140-G-A		not specified	Uncertain significance (Jun 01, 2023)
4-158859193-T-G		not specified	Uncertain significance (Sep 14, 2022)
4-158859194-T-A		not specified	Uncertain significance (Sep 14, 2022)
4-158859236-G-A		not specified	Uncertain significance (Jun 09, 2022)
4-158859585-T-A		not specified	Uncertain significance (Jul 25, 2024)
4-158859639-G-A		not specified	Uncertain significance (Mar 01, 2024)
4-158861361-T-C		not specified	Uncertain significance (Jul 20, 2022)
4-158861448-A-G		not specified	Uncertain significance (Oct 03, 2022)
4-158861468-A-G		not specified	Uncertain significance (Feb 14, 2024)
4-158861630-C-T		not specified	Uncertain significance (May 17, 2023)
4-158861662-A-G		not specified	Uncertain significance (Jan 20, 2023)
4-158861711-G-C		not specified	Uncertain significance (Sep 27, 2024)
4-158861713-A-G		not specified	Uncertain significance (Jan 03, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FNIP2	protein_coding	protein_coding	ENST00000264433	17	138912

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	6.53e-7	124633	0	7	124640	0.0000281

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.28	517	606	0.854	0.0000325	7303
Missense in Polyphen		106	180.39	0.58761		2202
Synonymous	0.653	213	225	0.945	0.0000128	2178
Loss of Function	6.18	2	48.5	0.0413	0.00000255	581

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000557	0.0000556
Finnish	0.00	0.00
European (Non-Finnish)	0.0000266	0.0000265
Middle Eastern	0.0000557	0.0000556
South Asian	0.0000654	0.0000654
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a co-chaperone of HSP90AA1. Inhibits the ATPase activity of HSP90AA1 leading to reduction in its chaperone activity. Facilitates the binding of client protein FLCN to HSP90AA1 (PubMed:27353360). May play a role in the signal transduction pathway of apoptosis induced by O6-methylguanine- mispaired lesions (By similarity). May be involved in energy and/or nutrient sensing through the AMPK and mTOR signaling pathways (PubMed:18403135). May regulate phosphorylation of RPS6KB1 (PubMed:18663353). {ECO:0000250|UniProtKB:Q80TD3, ECO:0000269|PubMed:18403135, ECO:0000269|PubMed:18663353, ECO:0000269|PubMed:27353360}.
• Pathway: mTOR signaling pathway - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.0828

Intolerance Scores

• loftool: 0.243
• rvis_EVS: -0.1
• rvis_percentile_EVS: 45.65

Haploinsufficiency Scores

• pHI: 0.115
• hipred: Y
• hipred_score: 0.547
• ghis: 0.451

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.175

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fnip2
• Phenotype: neoplasm; normal phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); renal/urinary system phenotype; homeostasis/metabolism phenotype; cellular phenotype

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;regulation of protein phosphorylation;protein phosphorylation;mitochondrion organization;intrinsic apoptotic signaling pathway in response to DNA damage;positive regulation of protein complex assembly;positive regulation of peptidyl-serine phosphorylation;TORC1 signaling;negative regulation of catalytic activity
• Cellular component: cytoplasm
• Molecular function: protein binding;ATPase inhibitor activity;chaperone binding