LRRFIP1

LRR binding FLII interacting protein 1

Basic information

Region (hg38): 2:237627587-237813682

Links

ENSG00000124831 ∙ NCBI:9208 ∙ OMIM:603256 ∙ HGNC:6702 ∙ Uniprot:Q32MZ4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• schizophrenia (No Known Disease Relationship), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LRRFIP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRRFIP1 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				3	1	4
missense			48	1		49
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	48	4	1

Variants in LRRFIP1

This is a list of pathogenic ClinVar variants found in the LRRFIP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-237692491-C-G		not specified	Uncertain significance (Feb 15, 2023)
2-237692492-G-A		not specified	Uncertain significance (Nov 09, 2021)
2-237692504-C-T		not specified	Uncertain significance (Aug 17, 2022)
2-237692511-C-A		not specified	Uncertain significance (Mar 14, 2023)
2-237708568-C-T		not specified	Uncertain significance (Dec 18, 2023)
2-237708572-C-T		not specified	Uncertain significance (May 24, 2023)
2-237708578-G-A		Myoepithelial tumor	Uncertain significance (Nov 01, 2022)
2-237708592-G-A		not specified	Uncertain significance (Jul 13, 2022)
2-237708599-G-A		not specified	Uncertain significance (May 10, 2024)
2-237708611-T-C		not specified	Uncertain significance (Jul 09, 2021)
2-237719551-C-T		not specified	Uncertain significance (Sep 07, 2022)
2-237720791-G-A		not specified	Uncertain significance (May 15, 2024)
2-237720803-G-A		not specified	Uncertain significance (May 21, 2024)
2-237749212-T-A		not specified	Uncertain significance (Mar 07, 2024)
2-237749292-A-G		not specified	Uncertain significance (May 28, 2024)
2-237749309-C-T			Benign (Mar 29, 2018)
2-237751207-A-G		not specified	Uncertain significance (Apr 08, 2024)
2-237751222-A-G		not specified	Uncertain significance (May 13, 2024)
2-237753348-A-G		not specified	Uncertain significance (Sep 20, 2023)
2-237753439-A-G		not specified	Uncertain significance (Sep 29, 2023)
2-237753464-C-T			Likely benign (Mar 01, 2023)
2-237756119-C-A		not specified	Uncertain significance (Jan 31, 2024)
2-237756138-A-G		not specified	Uncertain significance (Oct 26, 2022)
2-237760179-T-C		not specified	Uncertain significance (Aug 17, 2021)
2-237760188-C-T		not specified	Uncertain significance (May 11, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRRFIP1	protein_coding	protein_coding	ENST00000392000	11	186107

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0195	0.977	125736	0	11	125747	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.348	465	444	1.05	0.0000240	5355
Missense in Polyphen		133	137.92	0.96432		1639
Synonymous	0.0408	170	171	0.996	0.0000104	1468
Loss of Function	2.55	6	17.5	0.342	7.40e-7	234

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000907	0.0000905
Ashkenazi Jewish	0.00	0.00
East Asian	0.000116	0.000109
Finnish	0.0000928	0.0000924
European (Non-Finnish)	0.0000355	0.0000352
Middle Eastern	0.000116	0.000109
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional repressor which preferentially binds to the GC-rich consensus sequence (5'-AGCCCCCGGCG-3') and may regulate expression of TNF, EGFR and PDGFA. May control smooth muscle cells proliferation following artery injury through PDGFA repression. May also bind double-stranded RNA. Positively regulates Toll-like receptor (TLR) signaling in response to agonist probably by competing with the negative FLII regulator for MYD88-binding. {ECO:0000269|PubMed:10364563, ECO:0000269|PubMed:14522076, ECO:0000269|PubMed:16199883, ECO:0000269|PubMed:19265123, ECO:0000269|PubMed:9705290}.
• Pathway: Disease;LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production;Innate Immune System;Immune System;Signaling by FGFR in disease;Cytosolic sensors of pathogen-associated DNA ;Signaling by cytosolic FGFR1 fusion mutants;FGFR1 mutant receptor activation;Signaling by FGFR1 in disease;Diseases of signal transduction (Consensus)

Recessive Scores

• pRec: 0.0898

Intolerance Scores

• loftool: 0.827
• rvis_EVS: 0.61
• rvis_percentile_EVS: 82.96

Haploinsufficiency Scores

• pHI: 0.110
• hipred: N
• hipred_score: 0.324
• ghis: 0.526

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.947

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrrfip1

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;regulation of transcription by RNA polymerase II;positive regulation of type I interferon production;negative regulation of transcription, DNA-templated;positive regulation of NF-kappaB transcription factor activity
• Cellular component: nucleus;cytoplasm;cytosol;cytoskeleton;plasma membrane
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;DNA binding;double-stranded RNA binding;protein binding;protein homodimerization activity;cadherin binding