LRIG3

leucine rich repeats and immunoglobulin like domains 3, the group of I-set domain containing

Basic information

Region (hg38): 12:58872149-58920504

Links

ENSG00000139263 ∙ NCBI:121227 ∙ OMIM:608870 ∙ HGNC:30991 ∙ Uniprot:Q6UXM1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Transcripts

Transcript IDs starting with ENST are treated as Ensembl, all others as RefSeq. Showing 4 of 9.

Transcript ID	Protein ID	Coding exons	MANE Select	MANE Plus Clinical
NM_153377.5	NP_700356.2	19	yes	-
ENST00000320743.8	ENSP00000326759.3	19	yes	-
NM_001136051.3	NP_001129523.1	19	-	-
ENST00000379141.8	ENSP00000368436.4	19	-	-

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LRIG3 gene.

• not_specified (140 variants)
• not_provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRIG3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_153377.5. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2		2
missense			138	6		144
nonsense			1			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1			1
Total	0	0	140	8	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRIG3	protein_coding	protein_coding	ENST00000320743	19	48373

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
		125676	0	72	125748	0.000286

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.16	529	610	0.868	0.0000318	7341
Missense in Polyphen		179	238.97	0.74905		2883
Synonymous	-0.131	237	234	1.01	0.0000129	2171
Loss of Function	3.63	24	52.4	0.458	0.00000280	612

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00112	0.00112
Ashkenazi Jewish	0.00	0.00
East Asian	0.000219	0.000217
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000283	0.000281
Middle Eastern	0.000219	0.000217
South Asian	0.000262	0.000261
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in craniofacial and inner ear morphogenesis during embryonic development. May act within the otic vesicle epithelium to control formation of the lateral semicircular canal in the inner ear, possibly by restricting the expression of NTN1 (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.125

Intolerance Scores

• loftool: 0.629
• rvis_EVS: -0.72
• rvis_percentile_EVS: 14.26

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.332

Gene Damage Prediction

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

Gene ontology

• Biological process: otolith morphogenesis
• Cellular component: extracellular space;plasma membrane;integral component of membrane;cytoplasmic vesicle membrane;extracellular matrix