LRRC1

leucine rich repeat containing 1

Basic information

Region (hg38): 6:53794497-53924125

Links

ENSG00000137269 ∙ NCBI:55227 ∙ OMIM:608195 ∙ HGNC:14307 ∙ Uniprot:Q9BTT6 ∙ 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 LRRC1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRRC1 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			25		1	26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	0	2

Variants in LRRC1

This is a list of pathogenic ClinVar variants found in the LRRC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-53795288-A-G		not specified	Uncertain significance (Nov 21, 2022)
6-53795303-G-T			Benign (Mar 02, 2018)
6-53795360-C-T		not specified	Uncertain significance (Dec 17, 2021)
6-53842185-G-T		not specified	Uncertain significance (Feb 16, 2023)
6-53879014-G-T		not specified	Uncertain significance (Aug 28, 2023)
6-53896863-G-A		not specified	Uncertain significance (Nov 10, 2022)
6-53897320-T-A		not specified	Uncertain significance (Mar 18, 2024)
6-53899767-C-A		not specified	Uncertain significance (Nov 17, 2023)
6-53899787-C-G		not specified	Uncertain significance (Oct 26, 2022)
6-53899796-G-A		not specified	Uncertain significance (Apr 25, 2022)
6-53899852-A-G		not specified	Uncertain significance (May 14, 2024)
6-53902634-C-G		not specified	Uncertain significance (Feb 16, 2023)
6-53902695-T-C		not specified	Uncertain significance (Mar 11, 2024)
6-53902707-A-G		not specified	Uncertain significance (Sep 12, 2023)
6-53904395-T-C		not specified	Uncertain significance (Oct 21, 2021)
6-53904435-A-C		not specified	Uncertain significance (Apr 11, 2023)
6-53913860-G-A		not specified	Uncertain significance (Dec 07, 2021)
6-53913902-C-A		not specified	Uncertain significance (Oct 27, 2021)
6-53913909-G-A		not specified	Uncertain significance (Feb 07, 2023)
6-53919515-T-C		not specified	Uncertain significance (Jan 03, 2024)
6-53919665-G-C		not specified	Uncertain significance (Nov 29, 2023)
6-53920633-C-T		not specified	Uncertain significance (Dec 22, 2023)
6-53920667-A-G		not specified	Uncertain significance (Mar 21, 2022)
6-53920694-G-A		not specified	Uncertain significance (May 12, 2024)
6-53920726-G-A		not specified	Uncertain significance (Nov 30, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRRC1	protein_coding	protein_coding	ENST00000370888	14	129625

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.932	0.0682	125739	0	9	125748	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.46	204	272	0.751	0.0000139	3360
Missense in Polyphen		51	92.858	0.54923		1152
Synonymous	0.0373	108	108	0.995	0.00000530	1042
Loss of Function	4.29	5	30.6	0.163	0.00000171	368

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000937	0.0000905
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.0000446	0.0000439
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.132

Intolerance Scores

• loftool: 0.280
• rvis_EVS: -0.4
• rvis_percentile_EVS: 26.73

Haploinsufficiency Scores

• pHI: 0.272
• hipred: Y
• hipred_score: 0.554
• ghis: 0.563

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.934

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrrc1

Gene ontology

• Cellular component: cytosol;membrane