LRRFIP2

LRR binding FLII interacting protein 2

Basic information

Region (hg38): 3:37052625-37183689

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.

• Inborn genetic diseases (29 variants)
• not provided (2 variants)
• Lynch syndrome (1 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.

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			28	1	2	31
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	28	1	3

Variants in LRRFIP2

This is a list of pathogenic ClinVar variants found in the LRRFIP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-37053579-C-T		Lynch syndrome	Benign (Sep 05, 2013)
3-37053856-G-C		not specified	Uncertain significance (May 23, 2023)
3-37053900-C-T		not specified	Uncertain significance (Oct 06, 2021)
3-37054508-C-T		not specified	Uncertain significance (Oct 26, 2021)
3-37055106-T-C		not specified	Uncertain significance (May 27, 2022)
3-37058860-C-A		not specified	Uncertain significance (Apr 11, 2023)
3-37058861-C-T		not specified	Uncertain significance (Apr 11, 2023)
3-37058868-A-C			Benign (Feb 26, 2018)
3-37058876-C-T		not specified	Uncertain significance (Jun 28, 2022)
3-37065866-G-C		not specified	Uncertain significance (Nov 09, 2021)
3-37065905-T-C		not specified	Uncertain significance (Sep 26, 2022)
3-37066306-T-C		not specified	Uncertain significance (Dec 01, 2022)
3-37091505-C-T		not specified	Uncertain significance (Jan 07, 2022)
3-37091508-C-T		not specified	Uncertain significance (Feb 28, 2023)
3-37094793-C-T		not specified	Uncertain significance (Dec 03, 2021)
3-37096621-T-G		not specified	Uncertain significance (Feb 22, 2023)
3-37102931-A-G			Benign (Feb 26, 2018)
3-37103001-C-A		not specified	Uncertain significance (Apr 19, 2023)
3-37105468-C-T		not specified	Likely benign (Feb 14, 2024)
3-37105489-G-C		not specified	Uncertain significance (Mar 29, 2022)
3-37108075-C-T		not specified	Uncertain significance (Mar 16, 2022)
3-37108086-C-T		not specified	Uncertain significance (May 31, 2023)
3-37108090-C-A		not specified	Uncertain significance (Mar 23, 2023)
3-37108671-T-C		not specified	Likely benign (Mar 29, 2022)
3-37109670-T-C		not specified	Uncertain significance (Jun 30, 2023)

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