LRRC46

leucine rich repeat containing 46

Basic information

Region (hg38): 17:47831634-47837719

Links

ENSG00000141294 ∙ NCBI:90506 ∙ ∙ HGNC:25047 ∙ Uniprot:Q96FV0 ∙ 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 LRRC46 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRRC46 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			19	1		20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	1	0

Variants in LRRC46

This is a list of pathogenic ClinVar variants found in the LRRC46 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-47832172-C-G		not specified	Uncertain significance (Jun 30, 2022)
17-47834433-C-T		not specified	Uncertain significance (Jun 18, 2024)
17-47834442-A-C		not specified	Uncertain significance (Jul 05, 2023)
17-47834456-C-T		not specified	Uncertain significance (Nov 30, 2021)
17-47834465-C-T		not specified	Uncertain significance (Aug 15, 2023)
17-47834466-G-A		not specified	Uncertain significance (Apr 24, 2023)
17-47835353-A-C		not specified	Uncertain significance (Oct 25, 2023)
17-47835696-G-T		not specified	Uncertain significance (Aug 04, 2023)
17-47836038-T-A		not specified	Uncertain significance (Mar 04, 2024)
17-47836049-C-A		not specified	Uncertain significance (Jan 18, 2022)
17-47836404-C-T		not specified	Uncertain significance (Aug 15, 2023)
17-47836464-G-A		not specified	Uncertain significance (Feb 12, 2024)
17-47836473-G-A		not specified	Uncertain significance (Nov 12, 2021)
17-47836857-G-A		not specified	Likely benign (Feb 02, 2024)
17-47836914-C-T		not specified	Uncertain significance (Dec 20, 2023)
17-47836941-G-A		not specified	Uncertain significance (Jan 03, 2024)
17-47837004-G-T		not specified	Uncertain significance (Jan 22, 2024)
17-47837005-G-A		not specified	Uncertain significance (Jun 18, 2021)
17-47837033-G-T		not specified	Uncertain significance (Mar 05, 2024)
17-47837034-G-T		not specified	Uncertain significance (Mar 05, 2024)
17-47837089-C-T		not specified	Uncertain significance (Mar 02, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRRC46	protein_coding	protein_coding	ENST00000269025	8	6087

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00110	0.957	125499	2	246	125747	0.000987

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.854	148	180	0.821	0.00000974	2076
Missense in Polyphen		39	45.18	0.86322		498
Synonymous	1.03	63	74.3	0.847	0.00000390	662
Loss of Function	1.79	7	14.3	0.489	7.06e-7	160

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00179	0.00178
Ashkenazi Jewish	0.00685	0.00677
East Asian	0.00440	0.00441
Finnish	0.00	0.00
European (Non-Finnish)	0.000308	0.000308
Middle Eastern	0.00440	0.00441
South Asian	0.000719	0.000686
Other	0.00163	0.00163

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.853
• rvis_EVS: -0.05
• rvis_percentile_EVS: 50.22

Haploinsufficiency Scores

• pHI: 0.0667
• hipred: N
• hipred_score: 0.123
• ghis: 0.447

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0195

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrrc46