CROCC

ciliary rootlet coiled-coil, rootletin

Basic information

Region (hg38): 1:16740273-16972964

Links

ENSG00000058453 ∙ NCBI:9696 ∙ OMIM:615776 ∙ HGNC:21299 ∙ Uniprot:Q5TZA2 ∙ 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 CROCC gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CROCC 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				17		17
missense			179	15	6	200
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2	1	3
non coding						0
Total	0	0	179	32	6

Variants in CROCC

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

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

Position	Type	Phenotype	Significance	ClinVar
1-16922041-C-T		not specified	Uncertain significance (Apr 23, 2024)
1-16922678-G-A		not specified	Uncertain significance (Jun 09, 2022)
1-16922706-C-T		not specified	Likely benign (Mar 06, 2023)
1-16922726-G-A		not specified	Uncertain significance (Mar 24, 2023)
1-16922757-G-A		not specified	Uncertain significance (Apr 18, 2023)
1-16922771-C-T		not specified	Uncertain significance (Feb 27, 2024)
1-16922784-A-G		not specified	Likely benign (Mar 27, 2023)
1-16922791-G-C		not specified	Uncertain significance (Jan 10, 2023)
1-16922795-C-A		not specified	Uncertain significance (Aug 05, 2024)
1-16924336-G-A		not specified	Uncertain significance (Jul 15, 2021)
1-16924341-A-G			Likely benign (Aug 22, 2018)
1-16924348-G-C		not specified	Uncertain significance (Nov 29, 2021)
1-16924403-G-A		not specified	Uncertain significance (Sep 14, 2022)
1-16924409-A-G		not specified	Uncertain significance (Nov 10, 2024)
1-16924429-C-T		not specified	Uncertain significance (Nov 24, 2024)
1-16924438-C-T		not specified	Uncertain significance (Oct 29, 2024)
1-16924466-C-G		not specified	Uncertain significance (Nov 11, 2024)
1-16924466-C-T		not specified	Uncertain significance (Mar 29, 2022)
1-16924471-A-G		not specified	Uncertain significance (Mar 19, 2024)
1-16929850-A-G		not specified	Uncertain significance (Oct 25, 2023)
1-16929861-C-T		not specified	Uncertain significance (Apr 27, 2022)
1-16929893-G-T		not specified	Uncertain significance (Sep 06, 2022)
1-16929897-A-G		not specified	Uncertain significance (Sep 26, 2024)
1-16929928-G-A		not specified	Uncertain significance (Dec 10, 2024)
1-16929955-C-T		not specified	Uncertain significance (Aug 21, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CROCC	protein_coding	protein_coding	ENST00000375541	37	232707

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.27e-24	1.00	125482	0	266	125748	0.00106

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.351	1171	1.14e+3	1.03	0.0000830	12245
Missense in Polyphen		325	314.06	1.0348		3285
Synonymous	-0.618	518	500	1.04	0.0000321	4208
Loss of Function	3.95	55	96.9	0.567	0.00000516	1087

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00332	0.00321
Ashkenazi Jewish	0.000306	0.000298
East Asian	0.00321	0.00316
Finnish	0.0000469	0.0000462
European (Non-Finnish)	0.00105	0.000950
Middle Eastern	0.00321	0.00316
South Asian	0.000779	0.000752
Other	0.000828	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Major structural component of the ciliary rootlet, a cytoskeletal-like structure in ciliated cells which originates from the basal body at the proximal end of a cilium and extends proximally toward the cell nucleus (By similarity). Furthermore, is required for the correct positioning of the cilium basal body relative to the cell nucleus, to allow for ciliogenesis (PubMed:27623382). Contributes to centrosome cohesion before mitosis (PubMed:16203858). {ECO:0000250|UniProtKB:Q8CJ40, ECO:0000269|PubMed:16203858, ECO:0000269|PubMed:27623382}.

Recessive Scores

• pRec: 0.158

Intolerance Scores

• loftool: 0.881
• rvis_EVS: 2.43
• rvis_percentile_EVS: 98.53

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.278
• ghis: 0.483

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.225

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Crocc
• Phenotype: immune system phenotype; respiratory system phenotype; vision/eye 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)

Gene ontology

• Biological process: centrosome cycle;protein localization;centriole-centriole cohesion;epithelial structure maintenance;ciliary basal body organization;protein localization to organelle;photoreceptor cell maintenance;positive regulation of cilium assembly;establishment of organelle localization;positive regulation of protein localization to cilium
• Cellular component: photoreceptor inner segment;centrosome;centriole;cytosol;plasma membrane;actin cytoskeleton;ciliary rootlet;extracellular exosome
• Molecular function: actin binding;structural molecule activity;protein binding;kinesin binding