CEP170

protein-coding

centrosomal protein 170

Gene summary

The product of this gene is a component of the centrosome, a non-membraneous organelle that functions as the major microtubule-organizing center in animal cells. During interphase, the encoded protein localizes to the sub-distal appendages of mature centrioles, which are microtubule-based structures thought to help organize centrosomes. During mitosis, the protein associates with spindle microtubules near the centrosomes. The protein interacts with and is phosphorylated by polo-like kinase 1, and functions in maintaining microtubule organization and cell morphology. The human genome contains a putative transcribed pseudogene. Several alternatively spliced transcript variants of this gene have been found, but the full-length nature of some of these variants has not been determined. [provided by RefSeq, Jul 2008]

Previous symbols:

KIAA0470

MANE transcript

NM_014812.3

Inheritance

—

ClinVar variants

U:212B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.1

Max pathogenic AF

—

Genomic locus

chr1:243,124,428-243,255,793

External References & Databases

Ensembl (ENSG00000143702)

Transcript & Mutation Effects

hg38 • Region Span ~131.4 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 CEP170 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 206

not providedTotal: 7

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_014812.3. 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				4 clinvar		4
missense			208 clinvar	2 clinvar		210
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	212	6	0	218

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 68 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_014812.3	RefSeq	NP_055627.2	19	MANE Select
ENST00000366542.6	Ensembl	ENSP00000355500.1	19	MANE Select
NM_001042404.2	RefSeq	NP_001035863.1	18	Standard
NM_001042405.2	RefSeq	NP_001035864.1	18	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

protein binding

Cellular Component

centrosome
centriole
spindle
cytosol
microtubule

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000366542
Coding exons: 19
Length: 130921
Individuals with no LoFs: 124625
Homozygous LoFs: 0
Heterozygous LoFs: 12
Defined: 124637
p: 0.0000481

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.20	593	764	0.776	0.0000396	10269
Missense (PolyPhen)		159	299.6	0.5307		3987
Synonymous	1.92	222	262	0.849	0.0000133	3040
Loss of Function	6.58	6	61.8	0.0970	0.00000357	846

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000069	0.000065	rare
Latino/Admixed American	0.000087	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00018	0.00017	rare
Finnish	0.000047	0.000046	rare
European (Non-Finnish)	0.000027	0.000027	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Plays a role in microtubule organization (PubMed:15616186). Required for centriole subdistal appendage assembly (PubMed:28422092). {ECO:0000269|PubMed:15616186, ECO:0000269|PubMed:28422092}.;

Recessive Scores

pRec: 0.130

Intolerance Scores

LoFtool: 0.871
RVIS EVS: -0.27
RVIS percentile EVS: 34.82

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.929

Gene Damage Prediction

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