CEND1

cell cycle exit and neuronal differentiation 1

Basic information

Region (hg38): 11:787115-790113

Links

ENSG00000184524 ∙ NCBI:51286 ∙ OMIM:608213 ∙ HGNC:24153 ∙ Uniprot:Q8N111 ∙ 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 CEND1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CEND1 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						0
missense			25	1		26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	1	0

Variants in CEND1

This is a list of pathogenic ClinVar variants found in the CEND1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-788137-C-T		not specified	Uncertain significance (Mar 14, 2023)
11-788138-G-A		not specified	Uncertain significance (Sep 16, 2021)
11-788192-C-T		not specified	Uncertain significance (Feb 21, 2024)
11-788198-C-G		not specified	Uncertain significance (Jun 09, 2022)
11-788236-C-T		not specified	Likely benign (Oct 19, 2024)
11-788251-C-T		not specified	Uncertain significance (Jan 06, 2023)
11-788261-C-A		not specified	Uncertain significance (Jan 01, 2025)
11-788275-G-A		not specified	Uncertain significance (Aug 13, 2021)
11-788275-G-C		not specified	Uncertain significance (Jan 15, 2025)
11-788276-C-T		not specified	Uncertain significance (Oct 18, 2021)
11-788279-C-T		not specified	Uncertain significance (Sep 04, 2024)
11-788280-G-T		not specified	Uncertain significance (Jan 15, 2025)
11-788305-G-T		not specified	Uncertain significance (Oct 12, 2021)
11-788309-C-T		not specified	Uncertain significance (Dec 05, 2024)
11-788312-C-T		not specified	Uncertain significance (Nov 17, 2022)
11-788321-T-G		not specified	Uncertain significance (Jun 24, 2022)
11-788335-G-A		not specified	Uncertain significance (Jan 10, 2023)
11-788369-C-G		not specified	Uncertain significance (Jun 22, 2021)
11-788375-C-T		not specified	Uncertain significance (Jan 29, 2025)
11-788407-G-A		not specified	Uncertain significance (Dec 15, 2023)
11-788417-C-A		not specified	Uncertain significance (Oct 29, 2021)
11-788423-G-T		not specified	Uncertain significance (Aug 05, 2024)
11-788425-G-A		not specified	Uncertain significance (Dec 03, 2024)
11-788438-C-T		not specified	Uncertain significance (Mar 25, 2024)
11-788486-C-T		not specified	Uncertain significance (Aug 04, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CEND1	protein_coding	protein_coding	ENST00000330106	1	3020

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.598	0.368	125037	0	4	125041	0.0000160

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.190	93	88.0	1.06	0.00000510	934
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000938	0.00000887
Middle Eastern	0.00	0.00
South Asian	0.0000990	0.0000980
Other	0.00	0.00

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.118
• hipred: N
• hipred_score: 0.241
• ghis: 0.700

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.580

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cend1
• Phenotype: cellular 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: adult walking behavior;biological_process;cerebellar granular layer maturation;cerebellar Purkinje cell differentiation;radial glia guided migration of cerebellar granule cell;negative regulation of cerebellar granule cell precursor proliferation;neuron differentiation
• Cellular component: mitochondrion;integral component of membrane;vesicle
• Molecular function: molecular_function;protein binding