LRRC4

protein-coding

leucine rich repeat containing 4, the group of I-set domain containing|Ig-like cell adhesion molecule family

Gene summary

Predicted to enable cell-cell adhesion mediator activity. Predicted to be involved in modulation of chemical synaptic transmission and synapse organization. Predicted to act upstream of or within synapse organization. Located in Golgi apparatus. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_022143.5

Inheritance

—

ClinVar variants

U:78B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr7:128,027,071-128,032,107

External References & Databases

Ensembl (ENSG00000128594)

Transcript & Mutation Effects

hg38 • Region Span ~5.0 kb

Loading mutation effect viewer...

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 LRRC4 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 75

not providedTotal: 7

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_022143.5. 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			75 clinvar	2 clinvar		77
nonsense			1 clinvar			1
start loss						0
frameshift			2 clinvar			2
splice donor/acceptor (+/-2bp)						0
Total	0	0	78	2	2	82

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 11 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_022143.5	RefSeq	NP_071426.1	1	MANE Select
ENST00000249363.4	Ensembl	ENSP00000249363.3	1	MANE Select
ENST00000476782.5	Ensembl	ENSP00000418093.1	1	Standard
ENST00000478726.1	Ensembl	ENSP00000417795.1	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Cell adhesion molecules (CAMs) - Homo sapiens (human)
Axon guidance - Homo sapiens (human)

Biological Process

modulation of chemical synaptic transmission
regulation of synapse organization
postsynaptic density protein 95 clustering
synaptic membrane adhesion

Molecular Function

protein binding

Cellular Component

cell junction
dendritic spine
excitatory synapse
Schaffer collateral - CA1 synapse
glutamatergic synapse

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000249363
Coding exons: 1
Length: 5037
Individuals with no LoFs: 125738
Homozygous LoFs: 0
Heterozygous LoFs: 4
Defined: 125742
p: 0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.96	287	397	0.723	0.0000245	4252
Missense (PolyPhen)		55	118.79	0.463		1365
Synonymous	-2.09	204	169	1.20	0.0000110	1392
Loss of Function	3.93	0	18.0	0.00	0.00000108	178

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000018	0.000018	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Synaptic adhesion protein. Regulates the formation of exitatory synapses through the recruitment of pre-and-postsynaptic proteins. Organize the lamina/pathway-specific differentiation of dendrites. Plays a important role for auditory synaptic responses. Involved in the suppression of glioma (By similarity). {ECO:0000250}.;

Recessive Scores

pRec: 0.148

Intolerance Scores

LoFtool: 0.0214
RVIS EVS: -0.24
RVIS percentile EVS: 36.17

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.245

Gene Damage Prediction

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