LRRC2

leucine rich repeat containing 2

Basic information

Region (hg38): 3:46515384-46606948

Links

ENSG00000163827 ∙ NCBI:79442 ∙ OMIM:607180 ∙ HGNC:14676 ∙ Uniprot:Q9BYS8 ∙ 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 LRRC2 gene.

• not provided (38 variants)
• Inborn genetic diseases (17 variants)
• CRIPTO-related condition (1 variants)
• not specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRRC2 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			14		4	18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			3	19	16	38
Total	0	0	17	19	20

Variants in LRRC2

This is a list of pathogenic ClinVar variants found in the LRRC2 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-46519036-A-G		not specified	Uncertain significance (Oct 03, 2022)
3-46521523-T-A		not specified	Uncertain significance (Jan 31, 2024)
3-46521542-A-G		not specified	Uncertain significance (Jan 11, 2023)
3-46521558-C-T		not specified	Uncertain significance (Aug 11, 2022)
3-46521578-C-T		not specified	Uncertain significance (Jan 16, 2024)
3-46521579-G-A			Benign (Apr 04, 2018)
3-46521635-G-A			Benign (Aug 10, 2017)
3-46527432-G-T		not specified	Uncertain significance (Oct 19, 2021)
3-46527436-T-G		not specified	Uncertain significance (Oct 19, 2021)
3-46527518-C-T		not specified	Uncertain significance (Sep 14, 2022)
3-46529911-A-G		not specified	Uncertain significance (Dec 21, 2023)
3-46529920-G-A		not specified	Uncertain significance (Oct 26, 2022)
3-46532864-A-G		not specified	Uncertain significance (Feb 22, 2023)
3-46532867-T-G			Benign (Apr 04, 2018)
3-46539063-G-A		not specified	Uncertain significance (Jan 08, 2024)
3-46539143-G-A		not specified	Uncertain significance (May 18, 2023)
3-46539186-A-T			Benign (Aug 10, 2017)
3-46545057-C-G		not specified	Uncertain significance (Nov 29, 2023)
3-46545090-G-A		not specified	Uncertain significance (Jan 26, 2022)
3-46545122-C-G		not specified	Uncertain significance (Jun 01, 2023)
3-46545158-C-T		not specified	Uncertain significance (Apr 19, 2023)
3-46545184-C-A		not specified	Uncertain significance (Jun 07, 2023)
3-46551477-C-T		not specified	Uncertain significance (Feb 10, 2023)
3-46551578-A-G		not specified	Uncertain significance (Jul 09, 2021)
3-46577270-A-C			Benign (Nov 27, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRRC2	protein_coding	protein_coding	ENST00000395905	8	64677

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.50e-7	0.670	125702	0	45	125747	0.000179

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.931	162	199	0.814	0.0000103	2468
Missense in Polyphen		46	57.167	0.80465		713
Synonymous	-0.848	85	75.6	1.12	0.00000404	671
Loss of Function	1.12	12	17.0	0.706	7.15e-7	233

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000337	0.000330
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000257	0.000255
Middle Eastern	0.000163	0.000163
South Asian	0.0000980	0.0000980
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0761

Intolerance Scores

• loftool: 0.850
• rvis_EVS: 1.24
• rvis_percentile_EVS: 93.35

Haploinsufficiency Scores

• pHI: 0.294
• hipred: N
• hipred_score: 0.261
• ghis: 0.389

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00223

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrrc2