LRRC40

protein-coding

leucine rich repeat containing 40

Gene summary

Predicted to be involved in intracellular signal transduction. Located in membrane. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_017768.5

Inheritance

—

ClinVar variants

U:78B:7

Top phenotype

Autism

gnomAD constraint

pLI —, LoF o/e 1

Max pathogenic AF

—

Genomic locus

chr1:70,144,805-70,205,579

External References & Databases

Ensembl (ENSG00000066557)

Transcript & Mutation Effects

hg38 • Region Span ~60.8 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 LRRC40 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 67

not providedTotal: 1

AutismTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_017768.5. 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			3 clinvar			3
missense			68 clinvar	7 clinvar		75
nonsense			1 clinvar			1
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	0	78	7	0	85

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 45 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_017768.5	RefSeq	NP_060238.3	15	MANE Select
ENST00000370952.4	Ensembl	ENSP00000359990.3	15	MANE Select
ENST00000861873.1	Ensembl	ENSP00000531932.1	15	Standard
ENST00000861873.2	Ensembl	ENSP00000531932.1	15	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Cellular Component

cytoplasm
membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000370952
Coding exons: 15
Length: 60816
Individuals with no LoFs: 125602
Homozygous LoFs: 0
Heterozygous LoFs: 146
Defined: 125748
p: 0.000581

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.185	287	296	0.970	0.0000145	3916
Missense (PolyPhen)		75	79.071	0.94851		1137
Synonymous	0.845	99	110	0.898	0.00000535	1154
Loss of Function	-0.00958	31	30.9	1.00	0.00000177	395

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00039	0.00037	rare
Latino/Admixed American	0.00049	0.00046	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.0015	0.0015	notable
Finnish	0.00070	0.00069	rare
European (Non-Finnish)	0.00046	0.00045	rare
South Asian	0.00096	0.00091	rare
Other	0.00053	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.101

Intolerance Scores

LoFtool: 0.901
RVIS EVS: 0.6
RVIS percentile EVS: 82.83

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.727

Gene Damage Prediction

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