LRRC38

leucine rich repeat containing 38

Basic information

Region (hg38): 1:13474973-13514003

Links

ENSG00000162494 ∙ NCBI:126755 ∙ OMIM:615212 ∙ HGNC:27005 ∙ Uniprot:Q5VT99 ∙ 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 LRRC38 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRRC38 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			14	4		18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	4	0

Variants in LRRC38

This is a list of pathogenic ClinVar variants found in the LRRC38 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-13475863-C-T		not specified	Uncertain significance (Aug 30, 2021)
1-13475877-G-A		not specified	Uncertain significance (Feb 05, 2024)
1-13475893-C-T		not specified	Uncertain significance (Sep 27, 2022)
1-13475959-C-T		not specified	Uncertain significance (Sep 22, 2023)
1-13475977-T-C		not specified	Uncertain significance (Mar 19, 2024)
1-13476046-G-A		not specified	Uncertain significance (Feb 16, 2023)
1-13476060-C-T		not specified	Uncertain significance (Dec 28, 2023)
1-13513056-A-T		not specified	Likely benign (Apr 07, 2023)
1-13513091-C-T		not specified	Likely benign (Apr 07, 2023)
1-13513100-C-T		not specified	Uncertain significance (Dec 03, 2021)
1-13513142-A-G		not specified	Uncertain significance (May 15, 2023)
1-13513157-T-G		not specified	Likely benign (Apr 07, 2023)
1-13513211-C-T		not specified	Uncertain significance (Dec 28, 2022)
1-13513268-A-T		not specified	Uncertain significance (Apr 24, 2024)
1-13513274-A-G		not specified	Likely benign (Apr 07, 2023)
1-13513332-T-C		not specified	Uncertain significance (Apr 21, 2022)
1-13513418-C-T		not specified	Uncertain significance (Dec 14, 2023)
1-13513419-G-A		not specified	Uncertain significance (Oct 02, 2023)
1-13513467-G-A		not specified	Uncertain significance (Sep 17, 2021)
1-13513581-C-G		not specified	Uncertain significance (Aug 30, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRRC38	protein_coding	protein_coding	ENST00000376085	2	39099

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.144	0.786	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.23	112	155	0.722	0.00000781	1898
Missense in Polyphen		39	57.827	0.67443		697
Synonymous	0.880	65	74.7	0.870	0.00000412	637
Loss of Function	1.47	2	5.84	0.343	2.52e-7	66

LoF frequencies by population

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

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}.

Recessive Scores

• pRec: 0.0981

Haploinsufficiency Scores

• pHI: 0.0964
• ghis: 0.484

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.160

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrrc38

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