LRIT1

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

Basic information

Region (hg38): 10:84231520-84241546

Previous symbols: [ "LRRC21" ]

Links

ENSG00000148602 ∙ NCBI:26103 ∙ OMIM:616103 ∙ HGNC:23404 ∙ Uniprot:Q9P2V4 ∙ 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 LRIT1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRIT1 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				1		1
missense			58	2		60
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	58	3	0

Variants in LRIT1

This is a list of pathogenic ClinVar variants found in the LRIT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-84231959-C-T		not specified	Uncertain significance (Jan 04, 2022)
10-84232034-G-A		not specified	Uncertain significance (Oct 27, 2023)
10-84232056-C-G		not specified	Uncertain significance (Sep 26, 2022)
10-84232082-T-C		not specified	Uncertain significance (Jan 29, 2024)
10-84232112-C-A		not specified	Uncertain significance (Aug 13, 2021)
10-84232190-T-C		not specified	Likely benign (Sep 27, 2021)
10-84232205-C-A		not specified	Uncertain significance (Mar 07, 2023)
10-84232252-T-C		not specified	Uncertain significance (May 18, 2022)
10-84232270-C-T		not specified	Uncertain significance (Mar 08, 2024)
10-84232282-C-T		not specified	Uncertain significance (Mar 25, 2022)
10-84232318-T-G		not specified	Uncertain significance (Nov 20, 2023)
10-84232349-T-A		not specified	Uncertain significance (Apr 25, 2023)
10-84232352-C-T		not specified	Uncertain significance (Aug 04, 2023)
10-84232354-C-G		not specified	Uncertain significance (Mar 17, 2023)
10-84232385-G-A		not specified	Uncertain significance (Apr 08, 2022)
10-84232422-G-C		not specified	Uncertain significance (Dec 17, 2023)
10-84232439-T-C		not specified	Uncertain significance (May 04, 2022)
10-84232510-A-G		not specified	Uncertain significance (Nov 08, 2022)
10-84232541-C-T		not specified	Uncertain significance (Feb 22, 2023)
10-84232549-T-C		not specified	Uncertain significance (May 04, 2022)
10-84232550-C-G		not specified	Uncertain significance (Jan 23, 2023)
10-84232631-C-G		not specified	Uncertain significance (Nov 08, 2022)
10-84232654-T-G		not specified	Uncertain significance (Mar 20, 2023)
10-84232666-A-G		not specified	Uncertain significance (Apr 15, 2024)
10-84232753-G-A		not specified	Uncertain significance (Feb 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRIT1	protein_coding	protein_coding	ENST00000372105	4	9869

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.59e-15	0.00668	125374	5	369	125748	0.00149

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.579	398	367	1.09	0.0000217	3966
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00877	0.00876
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.000928	0.000925
Finnish	0.00	0.00
European (Non-Finnish)	0.000682	0.000607
Middle Eastern	0.000928	0.000925
South Asian	0.000265	0.000261
Other	0.00102	0.000978

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.140
• hipred: N
• hipred_score: 0.238
• ghis: 0.391

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.128

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrit1
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); vision/eye phenotype

Gene ontology

• Biological process: biological_process
• Cellular component: integral component of endoplasmic reticulum membrane
• Molecular function: molecular_function