LRRC23

protein-coding

leucine rich repeat containing 23

Gene summary

Involved in flagellated sperm motility and radial spoke assembly. Located in cytoplasm and sperm flagellum. Implicated in spermatogenic failure 92. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001135217.2

Inheritance

ClinVar variants

P:2U:50B:2

Top phenotype

Spermatogenic failure 92

gnomAD constraint

pLI —, LoF o/e 0.78

Max pathogenic AF

—

Genomic locus

chr12:6,873,569-6,914,241

External References & Databases

Ensembl (ENSG00000010626)

Transcript & Mutation Effects

hg38 • Region Span ~40.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

spermatogenic failure 92MODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0970999

Submitter: PanelApp Australia

Clinical Genomic Database (CGD)

Spermatogenic failure 92AR

Manifestation: Genitourinary

Intervention: General

Rationale: 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

Refs: 37804054; 38091523

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to LRRC23 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 49

Spermatogenic failure 92Total: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001135217.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar			1
missense			48 clinvar	2 clinvar		50
nonsense	1 clinvar					1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)	1 clinvar		1 clinvar			2
Total	2	0	50	2	0	54

Highest pathogenic variant AF is 0.0000074344744

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 47 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001135217.2	RefSeq	NP_001128689.1	6	MANE Select
ENST00000443597.7	Ensembl	ENSP00000390932.2	6	MANE Select
NM_006992.4	RefSeq	NP_008923.1	6	Standard
NM_201650.3	RefSeq	NP_964013.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

biological_process

Molecular Function

molecular_function

Cellular Component

cellular_component
cytoplasm
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000007969
Coding exons: 6
Length: 40675
Individuals with no LoFs: 125685
Homozygous LoFs: 0
Heterozygous LoFs: 63
Defined: 125748
p: 0.000251

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.253	176	186	0.948	0.0000106	2237
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00031	0.00031	rare
Latino/Admixed American	0.000087	0.000087	rare
Ashkenazi Jewish	0.0012	0.0012	notable
East Asian	0.00054	0.00054	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00022	0.00022	rare
South Asian	0.00023	0.00023	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.117

Intolerance Scores

LoFtool: 0.947
RVIS EVS: -0.14
RVIS percentile EVS: 43.77

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.808

Gene Damage Prediction

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