LRRC24

leucine rich repeat containing 24, the group of I-set domain containing

Basic information

Region (hg38): 8:144522388-144527033

Links

ENSG00000254402 ∙ NCBI:441381 ∙ ∙ HGNC:28947 ∙ Uniprot:Q50LG9 ∙ 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 LRRC24 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRRC24 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				2		2
missense			31	2		33
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	31	4	0

Variants in LRRC24

This is a list of pathogenic ClinVar variants found in the LRRC24 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-144522527-G-C		not specified	Uncertain significance (Aug 02, 2023)
8-144522531-C-T		not specified	Uncertain significance (Nov 07, 2022)
8-144522563-G-T		not specified	Uncertain significance (Oct 27, 2022)
8-144522584-G-A		not specified	Uncertain significance (Feb 13, 2024)
8-144522618-C-T		not specified	Uncertain significance (Dec 11, 2023)
8-144522639-C-G		not specified	Uncertain significance (Mar 17, 2023)
8-144522698-C-T		not specified	Uncertain significance (Feb 05, 2024)
8-144522701-G-A		not specified	Uncertain significance (Apr 12, 2022)
8-144522713-G-A		not specified	Uncertain significance (Nov 21, 2022)
8-144522713-G-T		not specified	Uncertain significance (Apr 13, 2022)
8-144522725-C-T		not specified	Uncertain significance (Jun 18, 2021)
8-144522729-G-C		not specified	Uncertain significance (Jan 17, 2024)
8-144522745-C-G		not specified	Uncertain significance (Jun 16, 2023)
8-144522852-G-A		not specified	Uncertain significance (Nov 03, 2022)
8-144522861-C-G		not specified	Uncertain significance (Apr 18, 2024)
8-144522904-C-T			Likely benign (Sep 01, 2022)
8-144522921-G-A		not specified	Uncertain significance (May 23, 2024)
8-144523019-C-T		not specified	Uncertain significance (May 11, 2022)
8-144523035-C-A		not specified	Uncertain significance (Mar 08, 2024)
8-144523073-A-T		not specified	Uncertain significance (May 21, 2024)
8-144523109-C-T		not specified	Uncertain significance (Aug 12, 2021)
8-144523180-A-T			Likely benign (Oct 01, 2023)
8-144523200-G-T		not specified	Uncertain significance (Sep 22, 2023)
8-144523308-C-T		not specified	Uncertain significance (May 12, 2024)
8-144523328-C-T		not specified	Uncertain significance (Jun 19, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRRC24	protein_coding	protein_coding	ENST00000529415	4	4656

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000851	0.941	125268	0	28	125296	0.000112

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.678	295	264	1.12	0.0000153	3120
Missense in Polyphen		77	92.03	0.83669		1152
Synonymous	-3.51	180	129	1.39	0.00000730	1189
Loss of Function	1.67	7	13.7	0.512	7.57e-7	135

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000163	0.000153
Ashkenazi Jewish	0.00128	0.00120
East Asian	0.0000602	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000811	0.0000708
Middle Eastern	0.0000602	0.0000544
South Asian	0.000104	0.0000980
Other	0.000182	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.103

Haploinsufficiency Scores

• pHI: 0.187
• hipred: Y
• hipred_score: 0.580
• ghis: 0.416

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.571

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrrc24

Gene ontology

• Biological process: positive regulation of synapse assembly
• Cellular component: extracellular space;integral component of membrane;extracellular matrix