LCA5L

protein-coding

lebercilin LCA5 like

Gene summary

Predicted to be involved in intraciliary transport. Predicted to be active in axoneme. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C21orf13

MANE transcript

NM_152505.4

Inheritance

—

ClinVar variants

U:88B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.66

Max pathogenic AF

—

Genomic locus

chr21:39,405,728-39,445,805

External References & Databases

Ensembl (ENSG00000157578)

Transcript & Mutation Effects

hg38 • Region Span ~40.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to LCA5L variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 86

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_152505.4. 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				3 clinvar		3
missense			88 clinvar	1 clinvar		89
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	88	4	0	92

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 79 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_152505.4	RefSeq	NP_689718.1	7	MANE Select
ENST00000288350.8	Ensembl	ENSP00000288350.3	7	MANE Select
NM_001384285.1	RefSeq	NP_001371214.1	7	Standard
NM_001384286.1	RefSeq	NP_001371215.1	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

intraciliary transport

Molecular Function

protein binding

Cellular Component

axoneme

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000358268
Coding exons: 7
Length: 39962
Individuals with no LoFs: 125620
Homozygous LoFs: 0
Heterozygous LoFs: 125
Defined: 125745
p: 0.000497

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.513	304	330	0.920	0.0000153	4427
Missense (PolyPhen)		81	77.641	1.0433		1127
Synonymous	-0.316	126	122	1.04	0.00000606	1221
Loss of Function	1.40	13	19.7	0.660	9.55e-7	273

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0018	0.0018	notable
Latino/Admixed American	0.00041	0.00040	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00012	0.00011	rare
Finnish	0.00028	0.00028	rare
European (Non-Finnish)	0.00050	0.00047	rare
South Asian	0.00060	0.00059	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.870
RVIS EVS: 1.02
RVIS percentile EVS: 91.05

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.0632

Gene Damage Prediction

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