LRR1

leucine rich repeat protein 1, the group of Cyclophilin peptidylprolyl isomerases

Basic information

Region (hg38): 14:49598761-49614672

Previous symbols: [ "PPIL5" ]

Links

ENSG00000165501 ∙ NCBI:122769 ∙ OMIM:609193 ∙ HGNC:19742 ∙ Uniprot:Q96L50 ∙ 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 LRR1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRR1 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			35	3		38
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	35	3	0

Variants in LRR1

This is a list of pathogenic ClinVar variants found in the LRR1 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-49599055-G-A		not specified	Uncertain significance (Apr 08, 2024)
14-49599058-A-T		not specified	Uncertain significance (May 30, 2023)
14-49599169-C-G		not specified	Uncertain significance (Dec 07, 2021)
14-49599172-C-T		not specified	Uncertain significance (Nov 28, 2024)
14-49599177-A-C		not specified	Uncertain significance (Nov 07, 2024)
14-49602371-T-C		not specified	Uncertain significance (May 05, 2023)
14-49602425-C-G		not specified	Uncertain significance (Nov 14, 2024)
14-49602430-C-T		not specified	Uncertain significance (Jul 14, 2023)
14-49602431-G-T		not specified	Uncertain significance (Jun 25, 2024)
14-49602440-A-G		not specified	Uncertain significance (Jun 23, 2023)
14-49602443-C-T		not specified	Uncertain significance (Mar 07, 2024)
14-49602465-T-G		not specified	Uncertain significance (Jun 24, 2022)
14-49607416-T-C		not specified	Uncertain significance (Jun 22, 2024)
14-49607472-C-T		not specified	Uncertain significance (Oct 24, 2023)
14-49607499-A-T		not specified	Uncertain significance (Apr 18, 2023)
14-49607545-A-G		not specified	Uncertain significance (Aug 11, 2024)
14-49607592-C-T		not specified	Uncertain significance (Jan 10, 2023)
14-49607691-C-T		not specified	Uncertain significance (Nov 18, 2023)
14-49607710-A-C		not specified	Uncertain significance (Jan 17, 2023)
14-49607776-G-A		not specified	Uncertain significance (Jan 26, 2023)
14-49607820-A-C		not specified	Uncertain significance (Oct 14, 2023)
14-49607888-C-A		not specified	Uncertain significance (Nov 09, 2024)
14-49607889-G-A		not specified	Uncertain significance (Jan 16, 2024)
14-49607920-T-C		not specified	Uncertain significance (Nov 30, 2022)
14-49607935-A-G		not specified	Uncertain significance (Nov 09, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRR1	protein_coding	protein_coding	ENST00000298288	4	15976

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.11e-8	0.187	125637	0	111	125748	0.000441

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.305	202	215	0.941	0.0000102	2705
Missense in Polyphen		58	58.84	0.98572		777
Synonymous	-0.0110	81	80.9	1.00	0.00000377	816
Loss of Function	0.335	13	14.4	0.905	8.43e-7	187

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000695	0.000683
Ashkenazi Jewish	0.000409	0.000397
East Asian	0.000279	0.000272
Finnish	0.00	0.00
European (Non-Finnish)	0.000717	0.000677
Middle Eastern	0.000279	0.000272
South Asian	0.000264	0.000261
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May negatively regulate the 4-1BB-mediated signaling cascades which result in the activation of NK-kappaB and JNK1. Probable substrate recognition subunit of an ECS (Elongin BC- CUL2/5-SOCS-box protein) E3 ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins. {ECO:0000269|PubMed:15601820}.
• Pathway: Post-translational protein modification;Metabolism of proteins;Immune System;Adaptive Immune System;Antigen processing: Ubiquitination & Proteasome degradation;Class I MHC mediated antigen processing & presentation;Neddylation (Consensus)

Recessive Scores

• pRec: 0.0684

Intolerance Scores

• rvis_EVS: 0
• rvis_percentile_EVS: 53.85

Haploinsufficiency Scores

• pHI: 0.0750
• hipred: N
• hipred_score: 0.437
• ghis: 0.570

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrr1

Gene ontology

• Biological process: protein ubiquitination;post-translational protein modification
• Cellular component: cytosol
• Molecular function: protein binding