LCA5L

lebercilin LCA5 like

Basic information

Region (hg38): 21:39405728-39445805

Previous symbols: [ "C21orf13" ]

Links

ENSG00000157578 ∙ NCBI:150082 ∙ ∙ HGNC:1255 ∙ Uniprot:O95447 ∙ 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 LCA5L gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LCA5L 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				3		3
missense			46	1		47
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	46	4	0

Variants in LCA5L

This is a list of pathogenic ClinVar variants found in the LCA5L region.

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

Position	Type	Phenotype	Significance	ClinVar
21-39405910-G-A		not specified	Uncertain significance (Dec 17, 2023)
21-39405919-G-A		not specified	Uncertain significance (Aug 01, 2024)
21-39405959-C-T		not specified	Uncertain significance (Sep 14, 2021)
21-39405967-T-C		not specified	Uncertain significance (Oct 06, 2024)
21-39406013-T-C		not specified	Uncertain significance (Jan 20, 2023)
21-39406032-G-C			Likely benign (Apr 01, 2023)
21-39406057-T-G		not specified	Uncertain significance (Feb 28, 2025)
21-39406072-A-T		not specified	Uncertain significance (Jun 26, 2024)
21-39406099-A-G		not specified	Uncertain significance (Dec 11, 2024)
21-39406107-G-C		not specified	Uncertain significance (Jan 24, 2025)
21-39406173-A-G			Likely benign (Apr 01, 2023)
21-39406178-C-T		not specified	Uncertain significance (Aug 05, 2024)
21-39406225-T-C		not specified	Uncertain significance (Jan 24, 2025)
21-39406265-C-T		not specified	Uncertain significance (Jun 07, 2023)
21-39406310-C-G		not specified	Uncertain significance (Dec 16, 2023)
21-39406354-G-A		not specified	Uncertain significance (Nov 25, 2024)
21-39406359-G-C			Likely benign (Apr 01, 2023)
21-39406393-C-A		not specified	Uncertain significance (Jul 16, 2024)
21-39406393-C-G		not specified	Uncertain significance (Aug 17, 2021)
21-39406425-T-G		not specified	Uncertain significance (Nov 13, 2024)
21-39406469-T-C		not specified	Uncertain significance (Feb 08, 2025)
21-39406558-C-G		not specified	Uncertain significance (Nov 03, 2022)
21-39410003-C-T		not specified	Uncertain significance (Dec 19, 2023)
21-39410059-T-C		not specified	Uncertain significance (Sep 27, 2021)
21-39410068-T-G		not specified	Uncertain significance (Jun 22, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LCA5L	protein_coding	protein_coding	ENST00000358268	7	39962

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.46e-7	0.800	125620	0	125	125745	0.000497

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.513	304	330	0.920	0.0000153	4427
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00220	0.00219
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000119	0.000109
Finnish	0.000278	0.000277
European (Non-Finnish)	0.000496	0.000475
Middle Eastern	0.000119	0.000109
South Asian	0.000601	0.000588
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.870
• rvis_EVS: 1.02
• rvis_percentile_EVS: 91.05

Haploinsufficiency Scores

• pHI: 0.109
• hipred: N
• hipred_score: 0.123
• ghis: 0.394

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0632

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lca5l

Gene ontology

• Biological process: intraciliary transport
• Cellular component: axoneme
• Molecular function: protein binding