CEND1

protein-coding

cell cycle exit and neuronal differentiation 1

Gene summary

The protein encoded by this gene is a neuron-specific protein. The similar protein in pig enhances neuroblastoma cell differentiation in vitro and may be involved in neuronal differentiation in vivo. Multiple pseudogenes have been reported for this gene. [provided by RefSeq, Jul 2008]

MANE transcript

NM_016564.4

Inheritance

—

ClinVar variants

U:38B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr11:787,115-790,113

External References & Databases

Ensembl (ENSG00000184524)

Transcript & Mutation Effects

hg38 • Region Span ~3.0 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 CEND1 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 41

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_016564.4. 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						0
missense			38 clinvar	3 clinvar		41
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	38	3	0	41

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 10 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_016564.4	RefSeq	NP_057648.2	1	MANE Select
ENST00000330106.5	Ensembl	ENSP00000328336.4	1	MANE Select
ENST00000901135.1	Ensembl	ENSP00000571194.1	1	Standard
ENST00000901135.2	Ensembl	ENSP00000571194.1	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

adult walking behavior
biological_process
cerebellar granular layer maturation
cerebellar Purkinje cell differentiation
radial glia guided migration of cerebellar granule cell

Molecular Function

molecular_function
protein binding

Cellular Component

mitochondrion
integral component of membrane
vesicle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000330106
Coding exons: 1
Length: 3020
Individuals with no LoFs: 125037
Homozygous LoFs: 0
Heterozygous LoFs: 4
Defined: 125041
p: 0.0000160

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.190	93	88.0	1.06	0.00000510	934
Missense (PolyPhen)		25	23.248	1.0754		216
Synonymous	-0.818	51	44.1	1.16	0.00000336	338
Loss of Function	1.56	0	2.85	0.00	1.71e-7	36

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.0000094	0.0000089	rare
South Asian	0.000099	0.000098	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Involved in neuronal differentiation. {ECO:0000250|UniProtKB:Q9JKC6}.;

Recessive Scores

pRec: 0.106

Intolerance Scores

LoFtool: 0.0762
RVIS EVS: -0.21
RVIS percentile EVS: 38.28

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.580

Gene Damage Prediction

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