LRRFIP2

LRR binding FLII interacting protein 2

Basic information

Region (hg38): 3:37052626-37183689

Links

ENSG00000093167 ∙ NCBI:9209 ∙ OMIM:614043 ∙ HGNC:6703 ∙ Uniprot:Q9Y608 ∙ 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 LRRFIP2 gene.

• not_specified (82 variants)
• not_provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRRFIP2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000006309.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			79	2	2	83
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1			1
Total	0	0	80	3	2

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRRFIP2	protein_coding	protein_coding	ENST00000421307	27	131064

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.58e-25	0.0779	125607	0	141	125748	0.000561

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.713	348	387	0.898	0.0000206	4681
Missense in Polyphen		95	124.71	0.76176		1594
Synonymous	0.958	117	131	0.893	0.00000625	1304
Loss of Function	1.66	46	59.8	0.769	0.00000376	643

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00183	0.00183
Ashkenazi Jewish	0.0000995	0.0000992
East Asian	0.000441	0.000435
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000556	0.000545
Middle Eastern	0.000441	0.000435
South Asian	0.000691	0.000686
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May function as activator of the canonical Wnt signaling pathway, in association with DVL3, upstream of CTNNB1/beta- catenin. 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:15677333, ECO:0000269|PubMed:19265123}.

Recessive Scores

• pRec: 0.0964

Intolerance Scores

• loftool: 0.924
• rvis_EVS: -0.06
• rvis_percentile_EVS: 48.87

Haploinsufficiency Scores

• pHI: 0.127
• hipred: Y
• hipred_score: 0.522
• ghis: 0.501

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: K
• gene_indispensability_pred: E
• gene_indispensability_score: 0.810

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrrfip2

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;biological_process;Wnt signaling pathway
• Cellular component: cellular_component
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;protein binding;LRR domain binding