CEP76

protein-coding

centrosomal protein 76

Gene summary

This gene encodes a centrosomal protein which regulates centriole amplification by limiting centriole duplication to once per cell cycle. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2012]

Previous symbols:

C18orf9

MANE transcript

NM_024899.4

Inheritance

—

ClinVar variants

P:13U:82B:7

Top phenotype

CEP76-related disorder

gnomAD constraint

pLI —, LoF o/e 0.52

Max pathogenic AF

—

Genomic locus

chr18:12,661,833-12,702,777

External References & Databases

Ensembl (ENSG00000101624)

Transcript & Mutation Effects

hg38 • Region Span ~40.9 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 CEP76 variants in ClinVar

8 Conditions Cataloged

not specifiedTotal: 74

CEP76-related disorderTotal: 6

Joubert syndrome 1Total: 5

not providedTotal: 3

Short statureTotal: 3

See casesTotal: 3

Retinitis pigmentosaTotal: 3

Bardet-Biedl syndrome 1Total: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_024899.4. 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	1 clinvar			3 clinvar		4
missense	1 clinvar	8 clinvar	78 clinvar	2 clinvar	2 clinvar	91
nonsense			1 clinvar			1
start loss						0
frameshift		3 clinvar				3
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	2	11	82	5	2	102

Highest pathogenic variant AF is 0.00005204274

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 34 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_024899.4	RefSeq	NP_079175.2	12	MANE Select
ENST00000262127.7	Ensembl	ENSP00000262127.2	12	MANE Select
NM_001271989.2	RefSeq	NP_001258918.1	11	Standard
ENST00000423709.6	Ensembl	ENSP00000403074.1	11	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Regulation of PLK1 Activity at G2/M Transition
Recruitment of mitotic centrosome proteins and complexes
Loss of Nlp from mitotic centrosomes
Loss of proteins required for interphase microtubule organization from the centrosome
Centrosome maturation

Biological Process

G2/M transition of mitotic cell cycle
regulation of G2/M transition of mitotic cell cycle
regulation of centriole replication
ciliary basal body-plasma membrane docking

Molecular Function

protein binding

Cellular Component

centrosome
centriole
cytosol
protein-containing complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000262127
Coding exons: 12
Length: 40945
Individuals with no LoFs: 125677
Homozygous LoFs: 0
Heterozygous LoFs: 71
Defined: 125748
p: 0.000282

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.75	265	358	0.740	0.0000191	4246
Missense (PolyPhen)		54	104.45	0.51699		1223
Synonymous	1.31	104	122	0.850	0.00000621	1308
Loss of Function	2.75	20	38.4	0.521	0.00000246	419

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00058	0.00055	rare
Latino/Admixed American	0.00031	0.00029	rare
Ashkenazi Jewish	0.00020	0.00020	rare
East Asian	0.00022	0.00022	rare
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.00029	0.00029	rare
South Asian	0.00034	0.00033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Centrosomal protein involved in regulation of centriole duplication. Required to limit centriole duplication to once per cell cycle by preventing centriole reduplication. {ECO:0000269|PubMed:19460342}.;

Recessive Scores

pRec: 0.145

Intolerance Scores

LoFtool: 0.625
RVIS EVS: 0.26
RVIS percentile EVS: 70.44

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.599

Gene Damage Prediction

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