LRIG1

protein-coding

leucine rich repeats and immunoglobulin like domains 1, 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 hair cycle process; innervation; and otolith morphogenesis. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_015541.3

Inheritance

—

ClinVar variants

U:229B:56

Top phenotype

LRIG1-related disorder

gnomAD constraint

pLI —, LoF o/e 0.26

Max pathogenic AF

—

Genomic locus

chr3:66,378,797-66,501,263

External References & Databases

Ensembl (ENSG00000144749)

Transcript & Mutation Effects

hg38 • Region Span ~122.5 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 LRIG1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 228

LRIG1-related disorderTotal: 43

not providedTotal: 18

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015541.3. 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	20 clinvar	4 clinvar	26
missense			223 clinvar	21 clinvar	11 clinvar	255
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	229	41	15	285

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 88 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_015541.3	RefSeq	NP_056356.2	19	MANE Select
ENST00000273261.8	Ensembl	ENSP00000273261.3	19	MANE Select
NM_001377344.1	RefSeq	NP_001364273.1	18	Standard
NM_001377345.1	RefSeq	NP_001364274.1	14	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

EGF-Ncore
Signal Transduction
ErbB4 signaling events
Signaling by EGFR
Negative regulation of MET activity

Biological Process

sensory perception of sound
hair cycle process
otolith morphogenesis
innervation

Cellular Component

extracellular space
plasma membrane
integral component of membrane
extracellular matrix

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000273261
Coding exons: 19
Length: 122467
Individuals with no LoFs: 125484
Homozygous LoFs: 1
Heterozygous LoFs: 263
Defined: 125748
p: 0.00105

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-1.18	719	636	1.13	0.0000392	7077
Missense (PolyPhen)		130	166.52	0.78068		1948
Synonymous	-5.51	394	277	1.42	0.0000190	2250
Loss of Function	4.61	12	45.6	0.263	0.00000248	511

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00062	0.00062	rare
Latino/Admixed American	0.00023	0.00023	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0	0.0	absent
Finnish	0.0011	0.0011	notable
European (Non-Finnish)	0.0017	0.0016	notable
South Asian	0.00091	0.00088	rare
Other	0.0013	0.0013	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Acts as a feedback negative regulator of signaling by receptor tyrosine kinases, through a mechanism that involves enhancement of receptor ubiquitination and accelerated intracellular degradation. {ECO:0000269|PubMed:15282549}.;

Recessive Scores

pRec: 0.205

Intolerance Scores

LoFtool: 0.483
RVIS EVS: 0.33
RVIS percentile EVS: 73.54

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.965

Gene Damage Prediction

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