LRIG3

leucine rich repeats and immunoglobulin like domains 3, the group of I-set domain containing

Basic information

Region (hg38): 12:58872149-58920504

Links

ENSG00000139263 ∙ NCBI:121227 ∙ OMIM:608870 ∙ HGNC:30991 ∙ Uniprot:Q6UXM1 ∙ 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 LRIG3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRIG3 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		2
missense			74	3	1	78
nonsense						0
start loss						0
frameshift						0
inframe indel					1	1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	74	5	2

Variants in LRIG3

This is a list of pathogenic ClinVar variants found in the LRIG3 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-58872645-T-C		not specified	Uncertain significance (Aug 12, 2022)
12-58872693-C-A		not specified	Uncertain significance (Aug 10, 2024)
12-58872774-T-C		not specified	Uncertain significance (May 03, 2023)
12-58874072-G-A		not specified	Likely benign (Sep 30, 2024)
12-58874072-G-C		not specified	Uncertain significance (Apr 07, 2023)
12-58874094-G-A		not specified	Uncertain significance (Sep 14, 2022)
12-58874137-T-A		not specified	Uncertain significance (Aug 05, 2024)
12-58874156-T-C		not specified	Uncertain significance (Jan 21, 2025)
12-58874177-A-C		not specified	Uncertain significance (Dec 16, 2024)
12-58874218-G-T		not specified	Uncertain significance (Feb 21, 2024)
12-58874222-C-T		not specified	Likely benign (Aug 20, 2024)
12-58874226-C-T		not specified	Uncertain significance (Jun 26, 2024)
12-58874229-A-T		not specified	Uncertain significance (Dec 22, 2023)
12-58874259-A-G		not specified	Uncertain significance (Dec 28, 2024)
12-58874492-G-A		not specified	Uncertain significance (Jan 02, 2024)
12-58874510-C-T		not specified	Uncertain significance (Nov 09, 2022)
12-58874540-T-C		not specified	Uncertain significance (Nov 08, 2024)
12-58876446-A-T			Benign (Jul 20, 2018)
12-58876475-C-T		not specified	Uncertain significance (May 29, 2024)
12-58876497-CTGG-C			Benign (Dec 31, 2019)
12-58876541-T-C		not specified	Uncertain significance (Apr 18, 2024)
12-58876589-G-A		not specified	Uncertain significance (Jan 10, 2022)
12-58877415-T-C		not specified	Uncertain significance (Oct 21, 2024)
12-58877433-G-A		not specified	Uncertain significance (May 25, 2022)
12-58877445-A-G		not specified	Uncertain significance (Aug 30, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRIG3	protein_coding	protein_coding	ENST00000320743	19	48373

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.17e-9	1.00	125676	0	72	125748	0.000286

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.16	529	610	0.868	0.0000318	7341
Missense in Polyphen		179	238.97	0.74905		2883
Synonymous	-0.131	237	234	1.01	0.0000129	2171
Loss of Function	3.63	24	52.4	0.458	0.00000280	612

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00112	0.00112
Ashkenazi Jewish	0.00	0.00
East Asian	0.000219	0.000217
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000283	0.000281
Middle Eastern	0.000219	0.000217
South Asian	0.000262	0.000261
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in craniofacial and inner ear morphogenesis during embryonic development. May act within the otic vesicle epithelium to control formation of the lateral semicircular canal in the inner ear, possibly by restricting the expression of NTN1 (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.125

Intolerance Scores

• loftool: 0.629
• rvis_EVS: -0.72
• rvis_percentile_EVS: 14.26

Haploinsufficiency Scores

• pHI: 0.275
• hipred: Y
• hipred_score: 0.544
• ghis: 0.529

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.332

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrig3
• 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); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); skeleton phenotype; hearing/vestibular/ear phenotype; vision/eye phenotype; craniofacial phenotype; growth/size/body region phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: otolith morphogenesis
• Cellular component: extracellular space;plasma membrane;integral component of membrane;cytoplasmic vesicle membrane;extracellular matrix