LRIT2

protein-coding

leucine rich repeat, Ig-like and transmembrane domains 2, the group of I-set domain containing

Gene summary

Predicted to be located in membrane. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

LRRC22

MANE transcript

NM_001017924.5

Inheritance

—

ClinVar variants

U:102B:7

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.98

Max pathogenic AF

—

Genomic locus

chr10:84,220,571-84,225,544

External References & Databases

Ensembl (ENSG00000204033)

Transcript & Mutation Effects

hg38 • Region Span ~5.0 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 LRIT2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 107

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001017924.5. 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						0
missense			101 clinvar	7 clinvar		108
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	102	7	0	109

Loading ClinVar variants...

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_001017924.5	RefSeq	NP_001017924.1	3	MANE Select
ENST00000372113.7	Ensembl	ENSP00000361185.3	3	MANE Select
NM_001284223.1	RefSeq	NP_001271152.1	4	Standard
ENST00000538192.5	Ensembl	ENSP00000438264.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000372113
Coding exons: 3
Length: 5092
Individuals with no LoFs: 125564
Homozygous LoFs: 0
Heterozygous LoFs: 184
Defined: 125748
p: 0.000732

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-1.75	379	294	1.29	0.0000148	3545
Missense (PolyPhen)		101	82.526	1.2239		1108
Synonymous	-0.229	125	122	1.03	0.00000614	1173
Loss of Function	0.0547	13	13.2	0.984	6.49e-7	154

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0011	0.0010	notable
Latino/Admixed American	0.00058	0.00058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.0025	0.0025	notable
Finnish	0.00028	0.00028	rare
European (Non-Finnish)	0.00063	0.00063	rare
South Asian	0.00059	0.00059	rare
Other	0.00082	0.00081	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.943
RVIS EVS: -0.26
RVIS percentile EVS: 34.93

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.221

Gene Damage Prediction

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