LRIT2

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

Basic information

Region (hg38): 10:84220570-84225544

Previous symbols: [ "LRRC22" ]

Links

ENSG00000204033 ∙ NCBI:340745 ∙ ∙ HGNC:23443 ∙ Uniprot:A6NDA9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LRIT2 gene.

• Inborn genetic diseases (29 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRIT2 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			28	1		29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	28	1	0

Variants in LRIT2

This is a list of pathogenic ClinVar variants found in the LRIT2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
10-84221940-C-T		not specified	Uncertain significance (Nov 27, 2023)
10-84221969-A-G		not specified	Uncertain significance (Aug 02, 2022)
10-84222045-T-A		not specified	Uncertain significance (Jan 18, 2022)
10-84222056-G-C		not specified	Uncertain significance (May 27, 2022)
10-84222065-C-T		not specified	Uncertain significance (Jul 27, 2021)
10-84222080-C-T		not specified	Uncertain significance (Feb 15, 2023)
10-84222081-G-A		not specified	Likely benign (Aug 13, 2021)
10-84222111-C-T		not specified	Uncertain significance (May 23, 2023)
10-84222132-C-T		not specified	Uncertain significance (Dec 28, 2022)
10-84222134-C-T		not specified	Uncertain significance (Aug 22, 2023)
10-84222201-C-G		not specified	Uncertain significance (Aug 02, 2021)
10-84222306-G-A		not specified	Uncertain significance (Sep 13, 2023)
10-84222393-A-T		not specified	Uncertain significance (Nov 22, 2021)
10-84222410-G-A		not specified	Uncertain significance (Apr 12, 2022)
10-84222417-C-A		not specified	Uncertain significance (Feb 23, 2023)
10-84222467-C-T		not specified	Uncertain significance (Nov 15, 2021)
10-84222587-G-C		not specified	Uncertain significance (Jun 01, 2023)
10-84222588-C-A		not specified	Uncertain significance (Jul 14, 2021)
10-84222638-A-G		not specified	Uncertain significance (May 23, 2023)
10-84224360-G-C		not specified	Uncertain significance (Jul 12, 2022)
10-84224360-G-T		not specified	Uncertain significance (May 04, 2022)
10-84224422-T-A		not specified	Uncertain significance (Jan 24, 2023)
10-84224467-G-T		not specified	Uncertain significance (Jan 30, 2024)
10-84224504-G-C		not specified	Uncertain significance (May 26, 2022)
10-84224510-C-T		not specified	Uncertain significance (Feb 05, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRIT2	protein_coding	protein_coding	ENST00000372113	3	5092

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.22e-9	0.110	125564	0	184	125748	0.000732

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.75	379	294	1.29	0.0000148	3545
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00163	0.00162
Ashkenazi Jewish	0.00	0.00
East Asian	0.00250	0.00250
Finnish	0.000277	0.000277
European (Non-Finnish)	0.000633	0.000633
Middle Eastern	0.00250	0.00250
South Asian	0.000588	0.000588
Other	0.000815	0.000815

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.943
• rvis_EVS: -0.26
• rvis_percentile_EVS: 34.93

Haploinsufficiency Scores

• pHI: 0.0764
• hipred: N
• hipred_score: 0.144
• ghis: 0.492

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.221

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrit2

Gene ontology

• Cellular component: integral component of membrane