LRRC55

leucine rich repeat containing 55

Basic information

Region (hg38): 11:57181747-57191717

Links

ENSG00000183908 ∙ NCBI:219527 ∙ OMIM:615213 ∙ HGNC:32324 ∙ Uniprot:Q6ZSA7 ∙ 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 LRRC55 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRRC55 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			25	1		26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			3			3
Total	0	0	28	1	0

Variants in LRRC55

This is a list of pathogenic ClinVar variants found in the LRRC55 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-57181906-C-T		not specified	Likely benign (Jun 29, 2023)
11-57181963-G-A		not specified	Uncertain significance (Dec 14, 2021)
11-57181981-C-T		not specified	Uncertain significance (Oct 19, 2024)
11-57181987-G-A		not specified	Uncertain significance (May 27, 2022)
11-57182076-G-A		not specified	Uncertain significance (Jan 20, 2023)
11-57182089-C-T		not specified	Uncertain significance (Jun 07, 2023)
11-57182117-C-T		not specified	Uncertain significance (Mar 07, 2025)
11-57182133-C-G		not specified	Uncertain significance (Sep 03, 2024)
11-57182140-G-A		not specified	Uncertain significance (Oct 02, 2023)
11-57182155-C-T		not specified	Uncertain significance (Dec 17, 2024)
11-57182165-T-G		not specified	Uncertain significance (May 28, 2024)
11-57182186-G-A		not specified	Uncertain significance (May 06, 2024)
11-57182193-C-G		not specified	Uncertain significance (Oct 22, 2021)
11-57182197-G-A		not specified	Uncertain significance (May 02, 2024)
11-57182249-G-A		not specified	Uncertain significance (Jan 26, 2023)
11-57182267-C-T		not specified	Uncertain significance (Sep 27, 2024)
11-57182287-A-G		not specified	Uncertain significance (Mar 30, 2024)
11-57182300-T-G		not specified	Uncertain significance (Dec 28, 2022)
11-57182338-C-T		not specified	Uncertain significance (Jul 28, 2021)
11-57182373-C-G		not specified	Uncertain significance (Aug 02, 2021)
11-57182465-C-T		not specified	Uncertain significance (May 14, 2024)
11-57182477-G-C		not specified	Uncertain significance (Dec 16, 2022)
11-57182531-G-A		not specified	Uncertain significance (Jan 14, 2025)
11-57182602-G-A		not specified	Uncertain significance (Nov 13, 2024)
11-57187268-G-A		not specified	Uncertain significance (Feb 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRRC55	protein_coding	protein_coding	ENST00000497933	2	9971

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0378	0.932	125243	0	505	125748	0.00201

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.438	194	212	0.915	0.0000125	2222
Missense in Polyphen		61	90.43	0.67455		1017
Synonymous	-0.913	101	90.0	1.12	0.00000511	725
Loss of Function	1.88	4	10.6	0.377	7.11e-7	92

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00101	0.00101
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00681	0.00681
European (Non-Finnish)	0.00290	0.00290
Middle Eastern	0.000109	0.000109
South Asian	0.00	0.00
Other	0.00130	0.00130

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. {ECO:0000269|PubMed:22547800}.

Intolerance Scores

• loftool: 0.335
• rvis_EVS: -0.56
• rvis_percentile_EVS: 19.54

Haploinsufficiency Scores

• pHI: 0.157
• hipred: Y
• hipred_score: 0.536
• ghis: 0.575

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.110

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrrc55

Gene ontology

• Biological 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