LRRC41

leucine rich repeat containing 41

Basic information

Region (hg38): 1:46261195-46303616

Links

ENSG00000132128 ∙ NCBI:10489 ∙ OMIM:618753 ∙ HGNC:16917 ∙ Uniprot:Q15345 ∙ 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 LRRC41 gene.

• Inborn genetic diseases (172 variants)
• Hereditary breast ovarian cancer syndrome (5 variants)
• not provided (4 variants)
• Premature ovarian failure (2 variants)
• Non-Hodgkin lymphoma (1 variants)
• Familial cancer of breast (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRRC41 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			29	3		32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding		2	87	58	2	149
Total	0	2	116	61	2

Highest pathogenic variant AF is 0.0000263

Variants in LRRC41

This is a list of pathogenic ClinVar variants found in the LRRC41 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-46261204-G-T		Hereditary breast ovarian cancer syndrome	Likely benign (Apr 19, 2022)
1-46261261-A-G		not specified	Uncertain significance (Mar 31, 2023)
1-46261261-A-T		Hereditary breast ovarian cancer syndrome • not specified	Likely benign (Sep 04, 2022)
1-46261262-A-G		not specified	Likely benign (Nov 04, 2023)
1-46261264-G-T		not specified	Likely benign (Jan 26, 2022)
1-46261269-A-G		not specified	Uncertain significance (Aug 24, 2023)
1-46261270-T-A		not specified	Uncertain significance (Nov 11, 2023)
1-46261270-T-G		not specified	Uncertain significance (Aug 17, 2021)
1-46261271-G-T		not specified	Uncertain significance (Dec 10, 2021)
1-46261273-A-G		not specified	Uncertain significance (Oct 31, 2022)
1-46261274-C-T		not specified	Likely benign (Mar 16, 2022)
1-46261275-C-A		not specified	Uncertain significance (Oct 29, 2022)
1-46261278-C-T		not specified	Uncertain significance (Jun 21, 2023)
1-46261279-G-A		not specified	Uncertain significance (Oct 03, 2023)
1-46261279-G-T		not specified	Likely benign (Dec 12, 2022)
1-46261282-G-A		not specified	Likely benign (Feb 18, 2023)
1-46261290-G-A		not specified	Uncertain significance (Dec 24, 2022)
1-46261290-G-C		Non-Hodgkin lymphoma • not specified	Conflicting classifications of pathogenicity (Nov 23, 2022)
1-46261297-C-A		not specified	Uncertain significance (Nov 08, 2023)
1-46261299-C-G		not specified	Uncertain significance (Jul 15, 2022)
1-46261301-C-T		not specified	Likely benign (Feb 13, 2022)
1-46261304-C-T		not specified	Likely benign (Oct 29, 2020)
1-46261305-C-A		not specified	Uncertain significance (Oct 17, 2021)
1-46261306-T-C		not specified	Uncertain significance (Sep 30, 2021)
1-46261310-C-A		not specified	Likely benign (Jul 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRRC41	protein_coding	protein_coding	ENST00000343304	10	42413

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000140	125731	0	17	125748	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.08	300	492	0.609	0.0000305	5137
Missense in Polyphen		22	59.816	0.3678		660
Synonymous	0.867	173	188	0.920	0.00000934	1827
Loss of Function	5.09	2	34.1	0.0587	0.00000213	336

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000665	0.0000665
Ashkenazi Jewish	0.000335	0.000298
East Asian	0.0000575	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000893	0.0000703
Middle Eastern	0.0000575	0.0000544
South Asian	0.0000716	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable substrate recognition component of an ECS (Elongin BC-CUL2/5-SOCS-box protein) E3 ubiquitin 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)

Intolerance Scores

• loftool: 0.213
• rvis_EVS: -0.44
• rvis_percentile_EVS: 24.46

Haploinsufficiency Scores

• pHI: 0.170
• hipred: Y
• hipred_score: 0.785
• ghis: 0.548

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.973

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrrc41

Gene ontology

• Biological process: protein ubiquitination;post-translational protein modification
• Cellular component: nucleus;cytoplasm;cytosol;membrane
• Molecular function: protein homodimerization activity