LRRC23

leucine rich repeat containing 23

Basic information

Region (hg38): 12:6873569-6914241

Links

ENSG00000010626 ∙ NCBI:10233 ∙ ∙ HGNC:19138 ∙ Uniprot:Q53EV4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spermatogenic failure 92	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Genitourinary	37804054; 38091523

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LRRC23 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRRC23 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			17			17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	0	0

Variants in LRRC23

This is a list of pathogenic ClinVar variants found in the LRRC23 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-6905700-G-C		not specified	Uncertain significance (May 24, 2024)
12-6905860-C-G		not specified	Uncertain significance (May 04, 2023)
12-6905867-A-T		not specified	Uncertain significance (Mar 15, 2024)
12-6905894-T-C		not specified	Uncertain significance (Apr 05, 2023)
12-6905900-G-T		not specified	Uncertain significance (Jun 10, 2024)
12-6906438-C-T		not specified	Uncertain significance (Apr 26, 2024)
12-6906453-G-A		not specified	Uncertain significance (Jul 20, 2021)
12-6906519-T-C		not specified	Uncertain significance (Dec 28, 2022)
12-6906530-G-A		not specified	Uncertain significance (Jan 04, 2024)
12-6906537-G-A		not specified	Uncertain significance (Aug 12, 2021)
12-6906540-A-G		not specified	Uncertain significance (Mar 20, 2024)
12-6906548-C-G		not specified	Uncertain significance (Dec 06, 2023)
12-6906548-C-T		Spermatogenic failure 92	Pathogenic (Jun 03, 2024)
12-6906609-T-C		not specified	Uncertain significance (Sep 11, 2024)
12-6906630-C-T		not specified	Uncertain significance (Aug 07, 2024)
12-6907344-G-A		not specified	Uncertain significance (Oct 26, 2022)
12-6907446-G-A		Spermatogenic failure 92	Pathogenic (Jun 03, 2024)
12-6909917-G-A		not specified	Uncertain significance (Jun 28, 2023)
12-6909957-G-A		not specified	Uncertain significance (Feb 27, 2024)
12-6912738-T-C		not specified	Uncertain significance (Nov 17, 2022)
12-6912767-C-T		not specified	Uncertain significance (Dec 28, 2023)
12-6912771-G-A		not specified	Uncertain significance (May 15, 2024)
12-6912836-C-T		not specified	Uncertain significance (Jul 13, 2022)
12-6912855-A-G		not specified	Uncertain significance (Jun 22, 2023)
12-6912873-G-A		not specified	Uncertain significance (Jan 31, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRRC23	protein_coding	protein_coding	ENST00000007969	6	40675

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.84e-8	0.423	125685	0	63	125748	0.000251

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.253	176	186	0.948	0.0000106	2237
Missense in Polyphen		52	54.807	0.94878		679
Synonymous	0.406	71	75.5	0.941	0.00000390	668
Loss of Function	0.867	14	18.0	0.779	0.00000116	194

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000395	0.000394
Ashkenazi Jewish	0.00119	0.00119
East Asian	0.000544	0.000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000220	0.000220
Middle Eastern	0.000544	0.000544
South Asian	0.000229	0.000229
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.117

Intolerance Scores

• loftool: 0.947
• rvis_EVS: -0.14
• rvis_percentile_EVS: 43.77

Haploinsufficiency Scores

• pHI: 0.241
• hipred: N
• hipred_score: 0.196
• ghis: 0.503

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.808

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrrc23
• Phenotype: reproductive system phenotype

Gene ontology

• Biological process: biological_process
• Cellular component: cellular_component;cytoplasm;cytosol
• Molecular function: molecular_function