LRIT1

protein-coding

leucine rich repeat, Ig-like and transmembrane domains 1, the group of Fibronectin type III domain containing|I-set domain containing

Gene summary

Predicted to act upstream of or within phototransduction; synaptic signaling; and visual perception. Predicted to be located in dendrite. Predicted to be active in endoplasmic reticulum membrane. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

LRRC21

MANE transcript

NM_015613.3

Inheritance

—

ClinVar variants

U:107B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.09

Max pathogenic AF

—

Genomic locus

chr10:84,231,520-84,241,546

External References & Databases

Ensembl (ENSG00000148602)

Transcript & Mutation Effects

hg38 • Region Span ~10.0 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 LRIT1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 108

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015613.3. 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				3 clinvar		3
missense			107 clinvar	2 clinvar		109
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	107	5	0	112

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 4 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_015613.3	RefSeq	NP_056428.1	4	MANE Select
ENST00000372105.4	Ensembl	ENSP00000361177.3	4	MANE Select
ENST00001138857.1	Ensembl	ENSP00000809985.1	4	Standard
XM_011539626.3	RefSeq	XP_011537928.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

biological_process

Molecular Function

molecular_function

Cellular Component

integral component of endoplasmic reticulum membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000372105
Coding exons: 4
Length: 9869
Individuals with no LoFs: 125374
Homozygous LoFs: 5
Heterozygous LoFs: 369
Defined: 125748
p: 0.00149

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.579	398	367	1.09	0.0000217	3966
Missense (PolyPhen)		122	111.24	1.0968		1347
Synonymous	-0.0612	162	161	1.01	0.00000985	1371
Loss of Function	-0.366	21	19.3	1.09	0.00000113	193

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0010	0.00098	notable
Latino/Admixed American	0.0078	0.0074	notable
Ashkenazi Jewish	0.00030	0.00030	rare
East Asian	0.00093	0.00092	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00068	0.00061	rare
South Asian	0.00026	0.00026	rare
Other	0.0010	0.00098	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Possible role in phototransduction. {ECO:0000303|PubMed:10777785}.;

Recessive Scores

pRec: 0.113

Intolerance Scores

LoFtool: 0.899
RVIS EVS: -0.26
RVIS percentile EVS: 34.95

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.128

Gene Damage Prediction

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