CNTD1

cyclin N-terminal domain containing 1

Basic information

Region (hg38): 17:42798799-42811587

Previous symbols: [ "CNTD" ]

Links

ENSG00000176563 ∙ NCBI:124817 ∙ OMIM:618166 ∙ HGNC:26847 ∙ Uniprot:Q8N815 ∙ 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 CNTD1 gene.

• Inborn genetic diseases (14 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CNTD1 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			12	2		14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	2	0

Variants in CNTD1

This is a list of pathogenic ClinVar variants found in the CNTD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-42799074-G-A		not specified	Likely benign (May 11, 2022)
17-42799137-A-G		not specified	Uncertain significance (Aug 29, 2022)
17-42799198-C-T		not specified	Uncertain significance (Aug 21, 2023)
17-42799203-C-T		not specified	Uncertain significance (Jun 05, 2023)
17-42804290-G-C		not specified	Likely benign (Sep 17, 2021)
17-42804347-G-A		not specified	Uncertain significance (Jan 04, 2022)
17-42806784-T-G		not specified	Uncertain significance (Nov 09, 2021)
17-42806787-A-G		not specified	Uncertain significance (Mar 20, 2023)
17-42806812-T-C		not specified	Uncertain significance (Jul 26, 2022)
17-42807776-T-C		not specified	Uncertain significance (Feb 28, 2024)
17-42807801-G-A		not specified	Uncertain significance (Jan 31, 2023)
17-42809411-T-C		not specified	Uncertain significance (Nov 15, 2021)
17-42809494-G-A		not specified	Uncertain significance (Jun 03, 2022)
17-42809501-G-C		not specified	Uncertain significance (Aug 02, 2022)
17-42809510-A-T		not specified	Uncertain significance (Aug 08, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CNTD1	protein_coding	protein_coding	ENST00000588408	7	12796

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00454	0.989	125717	0	30	125747	0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.837	145	176	0.823	0.00000892	2131
Missense in Polyphen		21	40.788	0.51485		545
Synonymous	1.42	57	72.3	0.788	0.00000395	675
Loss of Function	2.41	7	18.0	0.389	0.00000104	186

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000116	0.000116
Ashkenazi Jewish	0.000798	0.000397
East Asian	0.000272	0.000272
Finnish	0.00	0.00
European (Non-Finnish)	0.000106	0.000105
Middle Eastern	0.000272	0.000272
South Asian	0.000164	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.583
• rvis_EVS: 0.26
• rvis_percentile_EVS: 70.26

Haploinsufficiency Scores

• pHI: 0.109
• hipred: N
• hipred_score: 0.283

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0429

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cntd1
• Phenotype: reproductive system phenotype; endocrine/exocrine gland phenotype; cellular phenotype

Gene ontology

• Biological process: reciprocal meiotic recombination;spermatogenesis