CROCC

protein-coding

ciliary rootlet coiled-coil, rootletin

Gene summary

Predicted to enable kinesin binding activity and structural molecule activity. Involved in several processes, including centriole-centriole cohesion; positive regulation of cilium assembly; and positive regulation of protein localization to cilium. Located in centriole; centrosome; and ciliary basal body. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_014675.5

Inheritance

—

ClinVar variants

U:511B:49

Top phenotype

Premature ovarian insufficiency

gnomAD constraint

pLI —, LoF o/e 0.57

Max pathogenic AF

—

Genomic locus

chr1:16,740,273-16,972,964

External References & Databases

Ensembl (ENSG00000058453)

Transcript & Mutation Effects

hg38 • Region Span ~232.7 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 CROCC variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 505

not providedTotal: 46

Premature ovarian insufficiencyTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_014675.5. 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			6 clinvar	20 clinvar		26
missense			496 clinvar	24 clinvar	5 clinvar	525
nonsense			5 clinvar			5
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	511	44	5	560

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 18 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_014675.5	RefSeq	NP_055490.4	37	MANE Select
ENST00000375541.10	Ensembl	ENSP00000364691.4	37	MANE Select
ENST00000445545.6	Ensembl	ENSP00000402626.2	24	Standard
ENST00000467715.2	Ensembl	ENSP00000478281.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

centrosome cycle
protein localization
centriole-centriole cohesion
epithelial structure maintenance
ciliary basal body organization

Molecular Function

actin binding
structural molecule activity
protein binding
kinesin binding

Cellular Component

photoreceptor inner segment
centrosome
centriole
cytosol
plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000375541
Coding exons: 37
Length: 232707
Individuals with no LoFs: 125482
Homozygous LoFs: 0
Heterozygous LoFs: 266
Defined: 125748
p: 0.00106

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.351	1171	1.14e+3	1.03	0.0000830	12245
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0024	0.0023	notable
Latino/Admixed American	0.00093	0.00090	rare
Ashkenazi Jewish	0.00031	0.00030	rare
East Asian	0.0032	0.0032	notable
Finnish	0.000047	0.000046	rare
European (Non-Finnish)	0.0010	0.00095	notable
South Asian	0.00078	0.00075	rare
Other	0.00083	0.00081	rare

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.225

Gene Damage Prediction

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