LRIG3

protein-coding

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

Gene summary

Predicted to enable signaling receptor activity. Predicted to be involved in sensory perception of sound. Predicted to act upstream of or within otolith morphogenesis. Located in obsolete extracellular space. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_153377.5

Inheritance

—

ClinVar variants

U:140B:8

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.46

Max pathogenic AF

—

Genomic locus

chr12:58,872,149-58,920,504

External References & Databases

Ensembl (ENSG00000139263)

Transcript & Mutation Effects

hg38 • Region Span ~48.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to LRIG3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 140

not providedTotal: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_153377.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				2 clinvar		2
missense			138 clinvar	6 clinvar		144
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	140	8	0	148

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 15 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_153377.5	RefSeq	NP_700356.2	19	MANE Select
ENST00000320743.8	Ensembl	ENSP00000326759.3	19	MANE Select
NM_001136051.3	RefSeq	NP_001129523.1	19	Standard
ENST00000379141.8	Ensembl	ENSP00000368436.4	19	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

otolith morphogenesis

Cellular Component

extracellular space
plasma membrane
integral component of membrane
cytoplasmic vesicle membrane
extracellular matrix

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000320743
Coding exons: 19
Length: 48373
Individuals with no LoFs: 125676
Homozygous LoFs: 0
Heterozygous LoFs: 72
Defined: 125748
p: 0.000286

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.16	529	610	0.868	0.0000318	7341
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00080	0.00080	rare
Latino/Admixed American	0.00032	0.00032	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00022	0.00022	rare
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.00028	0.00028	rare
South Asian	0.00026	0.00026	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.332

Gene Damage Prediction

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