LRIG1

leucine rich repeats and immunoglobulin like domains 1, the group of I-set domain containing

Basic information

Region (hg38): 3:66378797-66501263

Links

ENSG00000144749 ∙ NCBI:26018 ∙ OMIM:608868 ∙ HGNC:17360 ∙ Uniprot:Q96JA1 ∙ 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 LRIG1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRIG1 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				19	8	27
missense			81	13	18	112
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2		2
non coding					2	2
Total	0	0	81	32	28

Variants in LRIG1

This is a list of pathogenic ClinVar variants found in the LRIG1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-66380318-G-A		not specified	Uncertain significance (Aug 08, 2023)
3-66380358-G-T		not specified	Uncertain significance (Aug 19, 2023)
3-66380387-T-G		not specified • LRIG1-related disorder	Benign (Mar 29, 2016)
3-66380396-G-A		not specified	Uncertain significance (Jan 25, 2023)
3-66380403-C-T		not specified	Uncertain significance (Dec 21, 2022)
3-66380446-G-A		LRIG1-related disorder	Benign (Feb 19, 2019)
3-66380453-G-C		LRIG1-related disorder	Benign (Feb 21, 2019)
3-66380474-G-A		not specified	Uncertain significance (Nov 17, 2022)
3-66380483-G-T		not specified	Uncertain significance (Dec 08, 2023)
3-66380601-G-A		not specified	Uncertain significance (Dec 01, 2022)
3-66380631-C-T			Likely benign (Jul 31, 2018)
3-66380635-G-C		LRIG1-related disorder	Benign (Nov 11, 2019)
3-66380643-G-T		not specified	Uncertain significance (Aug 22, 2023)
3-66380646-A-G		not specified	Uncertain significance (Dec 06, 2023)
3-66380680-G-A		LRIG1-related disorder	Benign (May 15, 2018)
3-66380720-T-A			Likely benign (Feb 01, 2023)
3-66380733-G-A		not specified	Uncertain significance (Dec 06, 2023)
3-66380737-C-T		LRIG1-related disorder	Benign (Aug 09, 2019)
3-66380738-G-A		not specified	Uncertain significance (Feb 10, 2023)
3-66380750-G-T		not specified	Uncertain significance (Mar 31, 2024)
3-66380763-C-T		LRIG1-related disorder	Benign (Nov 06, 2019)
3-66380788-G-T		not specified	Uncertain significance (Mar 15, 2024)
3-66380813-C-G		not specified	Likely benign (Jul 25, 2023)
3-66380813-C-T		not specified	Uncertain significance (Jun 24, 2022)
3-66380824-G-A		LRIG1-related disorder	Likely benign (Mar 18, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRIG1	protein_coding	protein_coding	ENST00000273261	19	122467

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0350	0.965	125484	1	263	125748	0.00105

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.18	719	636	1.13	0.0000392	7077
Missense in Polyphen		130	166.52	0.78068		1948
Synonymous	-5.51	394	277	1.42	0.0000190	2250
Loss of Function	4.61	12	45.6	0.263	0.00000248	511

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000848	0.000847
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.00	0.00
Finnish	0.00106	0.00106
European (Non-Finnish)	0.00165	0.00164
Middle Eastern	0.00	0.00
South Asian	0.000915	0.000882
Other	0.00130	0.00130

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a feedback negative regulator of signaling by receptor tyrosine kinases, through a mechanism that involves enhancement of receptor ubiquitination and accelerated intracellular degradation. {ECO:0000269|PubMed:15282549}.
• Pathway: EGF-Ncore;Signal Transduction;ErbB4 signaling events;Signaling by EGFR;Negative regulation of MET activity;Signaling by MET;Signaling by Receptor Tyrosine Kinases;Internalization of ErbB1 (Consensus)

Recessive Scores

• pRec: 0.205

Intolerance Scores

• loftool: 0.483
• rvis_EVS: 0.33
• rvis_percentile_EVS: 73.54

Haploinsufficiency Scores

• pHI: 0.744
• hipred: Y
• hipred_score: 0.756
• ghis: 0.459

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.965

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrig1
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); endocrine/exocrine gland phenotype; craniofacial phenotype; cellular phenotype; homeostasis/metabolism phenotype; skeleton phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); normal phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); neoplasm; limbs/digits/tail phenotype; hearing/vestibular/ear phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); digestive/alimentary phenotype; vision/eye phenotype; immune system phenotype

Gene ontology

• Biological process: sensory perception of sound;hair cycle process;otolith morphogenesis;innervation
• Cellular component: extracellular space;plasma membrane;integral component of membrane;extracellular matrix