LRRC40

leucine rich repeat containing 40

Basic information

Region (hg38): 1:70144805-70205579

Links

ENSG00000066557 ∙ NCBI:55631 ∙ ∙ HGNC:26004 ∙ Uniprot:Q9H9A6 ∙ 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 LRRC40 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRRC40 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			23	2		25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	2	0

Variants in LRRC40

This is a list of pathogenic ClinVar variants found in the LRRC40 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-70145813-C-A		not specified	Uncertain significance (Jun 03, 2022)
1-70145813-C-T		not specified	Uncertain significance (Jun 27, 2023)
1-70145815-G-T		not specified	Uncertain significance (Jan 20, 2023)
1-70145868-G-C		not specified	Uncertain significance (Jul 12, 2023)
1-70148553-G-A		not specified	Uncertain significance (May 08, 2024)
1-70148603-C-G		not specified	Uncertain significance (Aug 15, 2023)
1-70151134-A-G		not specified	Uncertain significance (Aug 31, 2022)
1-70151149-G-A		not specified	Uncertain significance (Oct 04, 2022)
1-70159341-T-C		not specified	Uncertain significance (Mar 28, 2024)
1-70159388-G-A			Likely benign (Dec 31, 2019)
1-70175852-C-T		not specified	Likely benign (Jan 03, 2024)
1-70175853-G-A		not specified	Uncertain significance (Jan 31, 2023)
1-70175879-G-A		not specified	Uncertain significance (May 26, 2022)
1-70175927-T-C		not specified	Uncertain significance (Dec 06, 2021)
1-70175970-C-G		not specified	Uncertain significance (Apr 04, 2024)
1-70178897-T-C		not specified	Uncertain significance (Jan 26, 2022)
1-70178903-C-T		not specified	Uncertain significance (Sep 14, 2021)
1-70178954-G-A		not specified	Uncertain significance (Aug 04, 2021)
1-70181097-T-C		not specified	Likely benign (Apr 06, 2024)
1-70181124-T-C		not specified	Uncertain significance (Nov 13, 2023)
1-70181155-T-A		not specified	Uncertain significance (Aug 26, 2022)
1-70184826-T-C		not specified	Uncertain significance (Jun 06, 2023)
1-70184846-T-C		not specified	Uncertain significance (Apr 05, 2023)
1-70184889-C-G		not specified	Uncertain significance (Jan 10, 2023)
1-70184898-T-C		not specified	Uncertain significance (Mar 02, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRRC40	protein_coding	protein_coding	ENST00000370952	15	60816

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.00e-21	0.00161	125602	0	146	125748	0.000581

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.185	287	296	0.970	0.0000145	3916
Missense in Polyphen		75	79.071	0.94851		1137
Synonymous	0.845	99	110	0.898	0.00000535	1154
Loss of Function	-0.00958	31	30.9	1.00	0.00000177	395

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000886	0.000863
Ashkenazi Jewish	0.00	0.00
East Asian	0.00151	0.00147
Finnish	0.000705	0.000693
European (Non-Finnish)	0.000462	0.000448
Middle Eastern	0.00151	0.00147
South Asian	0.000961	0.000915
Other	0.000531	0.000489

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.101

Intolerance Scores

• loftool: 0.901
• rvis_EVS: 0.6
• rvis_percentile_EVS: 82.83

Haploinsufficiency Scores

• pHI: 0.475
• hipred: N
• hipred_score: 0.350
• ghis: 0.605

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.727

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrrc40

Gene ontology

• Cellular component: cytoplasm;membrane