CLUAP1

clusterin associated protein 1, the group of IFT-B2 complex|Cilia and flagella associated

Basic information

Region (hg38): 16:3500976-3539048

Links

ENSG00000103351 ∙ NCBI:23059 ∙ OMIM:616787 ∙ HGNC:19009 ∙ Uniprot:Q96AJ1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Leber congenital amaurosis (Limited), mode of inheritance: AR
• Leber congenital amaurosis 9 (Strong), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CLUAP1 gene.

• Toriello-Lacassie-Droste syndrome (1 variants)
• Leber congenital amaurosis (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLUAP1 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			2	61	5	68
missense	1		193	3	5	202
nonsense			6			6
start loss			2			2
frameshift			2			2
inframe indel			2			2
splice donor/acceptor (+/-2bp)			7			7
splice region			14	15	4	33
non coding			1	46	5	52
Total	1	0	215	110	15

Variants in CLUAP1

This is a list of pathogenic ClinVar variants found in the CLUAP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-3501067-TA-T			Uncertain significance (Aug 10, 2023)
16-3501069-T-C			Uncertain significance (Feb 14, 2023)
16-3501072-C-G			Uncertain significance (Aug 17, 2023)
16-3501075-T-C			Uncertain significance (Jan 29, 2021)
16-3501075-TCCGCGACCTCCGCAGTAAGGCAGCC-T			Uncertain significance (Aug 26, 2019)
16-3501080-G-C		not specified	Uncertain significance (Jun 16, 2024)
16-3501081-A-G			Uncertain significance (Aug 31, 2019)
16-3501082-C-T			Likely benign (Jun 13, 2022)
16-3501084-T-G			Uncertain significance (Oct 04, 2022)
16-3501086-C-T			Uncertain significance (Jan 21, 2023)
16-3501088-C-T			Uncertain significance (Jul 28, 2023)
16-3501094-G-A			Uncertain significance (Feb 24, 2022)
16-3501096-C-T			Uncertain significance (Oct 05, 2022)
16-3501098-GC-G			Benign (Apr 08, 2022)
16-3501103-G-A			Likely benign (Jun 04, 2023)
16-3501107-C-G			Benign (Jan 26, 2024)
16-3501109-C-T			Likely benign (Oct 05, 2022)
16-3504700-T-C			Likely benign (Apr 14, 2023)
16-3504703-T-C			Likely benign (Nov 05, 2021)
16-3504728-G-A			Uncertain significance (Nov 20, 2022)
16-3504731-A-G			Uncertain significance (Oct 24, 2023)
16-3504732-T-C			Uncertain significance (Nov 03, 2023)
16-3504740-G-A			Uncertain significance (Feb 01, 2022)
16-3504741-C-T		not specified	Uncertain significance (Nov 13, 2024)
16-3504748-A-G			Uncertain significance (Jan 23, 2020)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CLUAP1	protein_coding	protein_coding	ENST00000576634	12	38125

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000418	0.998	125718	0	30	125748	0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0449	229	231	0.992	0.0000123	2762
Missense in Polyphen		42	58.537	0.7175		784
Synonymous	-0.380	90	85.5	1.05	0.00000513	714
Loss of Function	2.76	10	24.9	0.402	0.00000135	296

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000254	0.000245
Ashkenazi Jewish	0.00	0.00
East Asian	0.000110	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000164	0.000158
Middle Eastern	0.000110	0.000109
South Asian	0.000133	0.000131
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for cilia biogenesis. Appears to function within the multiple intraflagellar transport complex B (IFT-B). Key regulator of hedgehog signaling. {ECO:0000250|UniProtKB:Q8R3P7}.
• Pathway: Intraflagellar transport;Cilium Assembly;Organelle biogenesis and maintenance (Consensus)

Recessive Scores

• pRec: 0.107

Intolerance Scores

• loftool: 0.654
• rvis_EVS: 0.18
• rvis_percentile_EVS: 66.07

Haploinsufficiency Scores

• pHI: 0.0610
• hipred: N
• hipred_score: 0.294
• ghis: 0.543

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.885

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cluap1
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); embryo phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); growth/size/body region phenotype; cellular phenotype; homeostasis/metabolism phenotype

Zebrafish Information Network

• Gene name: cluap1
• Affected structure: retinal rod cell
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: intraciliary transport involved in cilium assembly
• Cellular component: nucleoplasm;centrosome;cilium;intraciliary transport particle B;intracellular membrane-bounded organelle;ciliary tip
• Molecular function: protein binding