LRRC25

leucine rich repeat containing 25

Basic information

Region (hg38): 19:18391137-18397622

Links

ENSG00000175489 ∙ NCBI:126364 ∙ OMIM:607518 ∙ HGNC:29806 ∙ Uniprot:Q8N386 ∙ 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 LRRC25 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRRC25 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			20	1	1	22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	1	1

Variants in LRRC25

This is a list of pathogenic ClinVar variants found in the LRRC25 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-18392103-C-T		not specified	Uncertain significance (Jun 29, 2023)
19-18396242-T-C		not specified	Uncertain significance (Feb 23, 2023)
19-18396264-G-T			Benign (May 18, 2018)
19-18396278-G-A		not specified	Uncertain significance (Dec 14, 2022)
19-18396279-G-C		not specified	Uncertain significance (Apr 19, 2023)
19-18396289-G-T		not specified	Uncertain significance (May 18, 2023)
19-18396290-C-T		not specified	Uncertain significance (Oct 13, 2023)
19-18396302-T-C		not specified	Uncertain significance (Feb 27, 2024)
19-18396306-G-A		not specified	Uncertain significance (Nov 12, 2021)
19-18396308-G-A		not specified	Uncertain significance (Jun 22, 2024)
19-18396326-G-C		not specified	Uncertain significance (Oct 06, 2021)
19-18396363-G-C		not specified	Uncertain significance (Feb 27, 2024)
19-18396375-T-C		not specified	Uncertain significance (Dec 07, 2023)
19-18396383-C-T		not specified	Uncertain significance (Sep 26, 2023)
19-18396492-C-T		not specified	Uncertain significance (Feb 28, 2024)
19-18396534-T-C		not specified	Uncertain significance (Feb 11, 2022)
19-18396612-A-G		not specified	Uncertain significance (May 17, 2023)
19-18396663-C-T		not specified	Uncertain significance (Feb 28, 2024)
19-18396666-C-T		not specified	Uncertain significance (Aug 16, 2021)
19-18396800-T-C		not specified	Uncertain significance (Mar 19, 2024)
19-18396878-G-A		not specified	Uncertain significance (Aug 20, 2023)
19-18396929-G-A		not specified	Likely benign (Jan 16, 2024)
19-18396930-G-T		not specified	Uncertain significance (Jan 16, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRRC25	protein_coding	protein_coding	ENST00000339007	2	6474

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.945	0.0548	125703	0	2	125705	0.00000796

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.807	154	185	0.833	0.0000122	1944
Missense in Polyphen		9	24.686	0.36457		307
Synonymous	1.43	75	92.5	0.811	0.00000661	670
Loss of Function	2.81	0	9.16	0.00	6.63e-7	75

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)	0.0000183	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in the inhibition of RLR-mediated type I interferon signaling pathway by targeting DDX58/RIG-I for autophagic degradation. Interacts specifically with ISG15- associated DDX58 to promote interaction between DDX58 and the autophagic cargo receptor p62/SQSTM1 to mediate DDX58 degradation via selective autophagy (PubMed:29288164). Plays also a role in the inhibition of NF-kappa-B signaling pathway and inflammatory response by promoting the degradation of p65/RELA. {ECO:0000269|PubMed:12384430, ECO:0000269|PubMed:29044191, ECO:0000269|PubMed:29288164}.
• Pathway: Vitamin D Receptor Pathway (Consensus)

Recessive Scores

• pRec: 0.112

Intolerance Scores

• loftool: 0.243
• rvis_EVS: 0.73
• rvis_percentile_EVS: 86.08

Haploinsufficiency Scores

• pHI: 0.116
• hipred: N
• hipred_score: 0.370
• ghis: 0.414

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.467

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrrc25

Gene ontology

• Cellular component: cytoplasm;integral component of membrane
• Molecular function: protein binding