LRRC58

leucine rich repeat containing 58

Basic information

Region (hg38): 3:120324509-120349354

Links

ENSG00000163428 ∙ NCBI:116064 ∙ ∙ HGNC:26968 ∙ Uniprot:Q96CX6 ∙ 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 LRRC58 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRRC58 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			22	3		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	22	3	0

Variants in LRRC58

This is a list of pathogenic ClinVar variants found in the LRRC58 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-120331228-C-T		not specified	Likely benign (Dec 14, 2021)
3-120331288-G-C		not specified	Uncertain significance (Jul 08, 2022)
3-120331292-C-A		not specified	Uncertain significance (May 03, 2023)
3-120331303-G-C		not specified	Uncertain significance (May 15, 2024)
3-120331309-G-A		not specified	Uncertain significance (Jul 26, 2022)
3-120334957-T-A		not specified	Uncertain significance (Sep 13, 2023)
3-120335041-C-T		not specified	Uncertain significance (Aug 09, 2021)
3-120335057-C-T		not specified	Uncertain significance (Jun 24, 2022)
3-120335074-A-G		not specified	Uncertain significance (Jun 26, 2023)
3-120335948-T-C			Likely benign (Dec 01, 2022)
3-120348787-T-A		not specified	Uncertain significance (Jan 26, 2023)
3-120348813-G-T		not specified	Uncertain significance (Dec 19, 2022)
3-120348841-C-T		not specified	Uncertain significance (Dec 20, 2023)
3-120348888-C-T		not specified	Uncertain significance (Dec 17, 2023)
3-120348894-G-C		not specified	Uncertain significance (Jul 25, 2023)
3-120348925-T-C		not specified	Likely benign (Jun 11, 2021)
3-120348934-C-G		not specified	Uncertain significance (Jan 11, 2023)
3-120348961-T-C		not specified	Uncertain significance (Oct 17, 2023)
3-120348978-G-A		not specified	Uncertain significance (May 04, 2023)
3-120349003-T-C		not specified	Uncertain significance (Jun 11, 2024)
3-120349024-C-T		not specified	Uncertain significance (Dec 02, 2021)
3-120349032-T-C		not specified	Uncertain significance (Nov 07, 2022)
3-120349090-G-A		not specified	Uncertain significance (Nov 18, 2022)
3-120349128-C-G		not specified	Uncertain significance (Jul 14, 2021)
3-120349138-C-T		not specified	Uncertain significance (Jan 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRRC58	protein_coding	protein_coding	ENST00000295628	4	24831

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00366	0.959	124624	0	14	124638	0.0000562

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.50	119	175	0.681	0.00000871	2302
Missense in Polyphen		44	70.1	0.62767		854
Synonymous	1.23	58	71.2	0.814	0.00000323	794
Loss of Function	1.82	6	13.1	0.457	7.80e-7	171

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000782	0.0000646
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000579	0.0000556
Finnish	0.00	0.00
European (Non-Finnish)	0.0000728	0.0000619
Middle Eastern	0.0000579	0.0000556
South Asian	0.000131	0.000131
Other	0.000176	0.000165

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.111

Haploinsufficiency Scores

• pHI: 0.305
• hipred: Y
• hipred_score: 0.546
• ghis: 0.653

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.581

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrrc58