LRRC52

leucine rich repeat containing 52

Basic information

Region (hg38): 1:165544000-165563957

Links

ENSG00000162763 ∙ NCBI:440699 ∙ OMIM:615218 ∙ HGNC:32156 ∙ Uniprot:Q8N7C0 ∙ 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 LRRC52 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRRC52 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					1	1
missense			10	1	1	12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	1	2

Variants in LRRC52

This is a list of pathogenic ClinVar variants found in the LRRC52 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-165544303-C-A		not specified	Uncertain significance (May 23, 2023)
1-165544307-C-T		not specified	Uncertain significance (May 09, 2023)
1-165544358-T-G		not specified	Uncertain significance (Dec 17, 2023)
1-165544408-A-G		not specified	Uncertain significance (Apr 08, 2024)
1-165544432-G-A		not specified	Uncertain significance (Sep 16, 2021)
1-165544565-G-A		not specified	Likely benign (Apr 25, 2022)
1-165544612-C-T		not specified	Uncertain significance (Aug 13, 2021)
1-165544641-G-C			Benign (Mar 06, 2018)
1-165544787-C-G		not specified	Uncertain significance (Apr 01, 2024)
1-165544820-C-T		not specified	Uncertain significance (May 06, 2024)
1-165563580-G-A		not specified	Uncertain significance (Jun 21, 2023)
1-165563654-G-A		not specified	Uncertain significance (Nov 16, 2021)
1-165563655-C-T		not specified	Uncertain significance (Feb 16, 2023)
1-165563711-C-T			Benign (Mar 06, 2018)
1-165563771-C-T		not specified	Uncertain significance (Nov 07, 2022)
1-165563796-C-T		not specified	Uncertain significance (Sep 01, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRRC52	protein_coding	protein_coding	ENST00000294818	2	19955

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000732	0.304	125680	0	68	125748	0.000270

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0365	173	174	0.992	0.0000101	2034
Missense in Polyphen		42	48.77	0.86119		647
Synonymous	-1.27	93	78.6	1.18	0.00000488	654
Loss of Function	0.126	8	8.39	0.953	5.15e-7	94

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000633	0.000633
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000163	0.000163
Finnish	0.000508	0.000508
European (Non-Finnish)	0.000326	0.000316
Middle Eastern	0.000163	0.000163
South Asian	0.0000654	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Auxiliary protein of the large-conductance, voltage and calcium-activated potassium channel (BK alpha). Modulates gating properties by producing a marked shift in the BK channel's voltage dependence of activation in the hyperpolarizing direction, and in the absence of calcium. KCNU1 channel auxiliary protein. May modulate KCNU1 gating properties. {ECO:0000269|PubMed:22547800, ECO:0000269|PubMed:23129643}.

Intolerance Scores

• loftool: 0.585
• rvis_EVS: -0.09
• rvis_percentile_EVS: 46.92

Haploinsufficiency Scores

• pHI: 0.135
• hipred: N
• hipred_score: 0.146

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.228

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrrc52
• Phenotype: reproductive system phenotype

Gene ontology

• Biological process: reproductive process;potassium ion transmembrane transport;positive regulation of voltage-gated potassium channel activity
• Cellular component: integral component of plasma membrane;voltage-gated potassium channel complex
• Molecular function: voltage-gated potassium channel activity;ion channel binding;potassium channel activator activity