LRRC43

leucine rich repeat containing 43

Basic information

Region (hg38): 12:122167738-122203471

Links

ENSG00000158113 ∙ NCBI:254050 ∙ ∙ HGNC:28562 ∙ Uniprot:Q8N309 ∙ 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 LRRC43 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRRC43 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			32	3		35
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	32	3	0

Variants in LRRC43

This is a list of pathogenic ClinVar variants found in the LRRC43 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-122172456-C-T		not specified	Uncertain significance (Jul 06, 2021)
12-122172524-G-A		not specified	Uncertain significance (Apr 04, 2024)
12-122172531-C-T		not specified	Uncertain significance (Aug 02, 2021)
12-122172552-C-T		not specified	Uncertain significance (Nov 17, 2022)
12-122172588-T-C		not specified	Uncertain significance (Aug 17, 2022)
12-122172610-G-T		not specified	Uncertain significance (Aug 13, 2021)
12-122172614-A-G		not specified	Uncertain significance (Jun 12, 2023)
12-122172705-A-G		not specified	Uncertain significance (Jun 29, 2023)
12-122172724-G-A		not specified	Likely benign (Mar 07, 2024)
12-122172724-G-C		not specified	Likely benign (Feb 21, 2024)
12-122173846-C-T		not specified	Uncertain significance (Oct 05, 2023)
12-122173905-C-T		not specified	Uncertain significance (Sep 21, 2023)
12-122173908-G-C		not specified	Uncertain significance (Jul 08, 2022)
12-122173924-C-T		not specified	Likely benign (Sep 29, 2023)
12-122173983-G-A		not specified	Uncertain significance (Jan 22, 2024)
12-122183149-A-T		not specified	Uncertain significance (Apr 04, 2023)
12-122183169-T-A		not specified	Uncertain significance (Aug 21, 2023)
12-122183185-A-G		not specified	Uncertain significance (Feb 21, 2024)
12-122183191-G-T		not specified	Uncertain significance (Feb 21, 2024)
12-122183208-C-T		not specified	Uncertain significance (May 10, 2022)
12-122183239-G-A		not specified	Uncertain significance (Jun 17, 2024)
12-122183250-C-G		not specified	Uncertain significance (Apr 08, 2024)
12-122183253-A-C		not specified	Likely benign (May 31, 2023)
12-122183271-T-C		not specified	Uncertain significance (Oct 20, 2023)
12-122184528-C-T		not specified	Uncertain significance (Mar 31, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRRC43	protein_coding	protein_coding	ENST00000339777	12	35734

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.72e-15	0.0477	124628	0	185	124813	0.000741

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.163	377	386	0.977	0.0000239	4174
Missense in Polyphen		146	147.98	0.98665		1604
Synonymous	-0.733	195	182	1.07	0.0000123	1392
Loss of Function	0.586	24	27.3	0.879	0.00000134	325

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00110	0.00109
Ashkenazi Jewish	0.000200	0.000199
East Asian	0.000724	0.000723
Finnish	0.000140	0.000139
European (Non-Finnish)	0.00106	0.00105
Middle Eastern	0.000724	0.000723
South Asian	0.000528	0.000523
Other	0.000661	0.000495

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.926
• rvis_EVS: 0.4
• rvis_percentile_EVS: 76.49

Haploinsufficiency Scores

• pHI: 0.0509
• hipred: N
• hipred_score: 0.180
• ghis: 0.483

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.164

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrrc43