CDIP1

cell death inducing p53 target 1

Basic information

Region (hg38): 16:4510669-4538828

Previous symbols: [ "C16orf5" ]

Links

ENSG00000089486 ∙ NCBI:29965 ∙ OMIM:610503 ∙ HGNC:13234 ∙ Uniprot:Q9H305 ∙ 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 CDIP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDIP1 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			19			19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	19	1	0

Variants in CDIP1

This is a list of pathogenic ClinVar variants found in the CDIP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-4512469-G-A			Likely benign (Dec 01, 2022)
16-4512611-G-T		not specified	Uncertain significance (Oct 12, 2024)
16-4512792-C-G		not specified	Uncertain significance (Jul 27, 2024)
16-4512841-G-A		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
16-4512910-G-C		not specified	Uncertain significance (Jul 22, 2024)
16-4512942-C-T		not specified	Uncertain significance (Nov 17, 2022)
16-4512984-G-A		not specified	Uncertain significance (Jan 22, 2024)
16-4512984-G-T		not specified	Uncertain significance (Jan 24, 2025)
16-4512990-G-T		not specified	Uncertain significance (Dec 05, 2024)
16-4513004-G-A		not specified	Uncertain significance (Feb 27, 2024)
16-4513004-G-T		not specified	Uncertain significance (Oct 29, 2021)
16-4513020-G-A		not specified	Uncertain significance (Apr 03, 2023)
16-4513040-T-G		not specified	Uncertain significance (Jan 27, 2022)
16-4513717-C-G		not specified	Uncertain significance (Feb 16, 2023)
16-4513746-G-T		not specified	Uncertain significance (Feb 04, 2025)
16-4513786-G-A		not specified	Uncertain significance (Oct 06, 2024)
16-4513791-A-G		not specified	Uncertain significance (Feb 06, 2023)
16-4513836-G-C		not specified	Uncertain significance (Dec 11, 2024)
16-4513848-C-T		not specified	Uncertain significance (Dec 10, 2024)
16-4514049-G-C		not specified	Uncertain significance (Jan 23, 2025)
16-4514078-A-G		not specified	Uncertain significance (Mar 18, 2024)
16-4514091-T-C		not specified	Uncertain significance (Jan 08, 2024)
16-4514093-G-A		not specified	Uncertain significance (Jun 18, 2021)
16-4514105-T-C		not specified	Uncertain significance (Dec 20, 2023)
16-4514112-G-C		not specified	Uncertain significance (Jan 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDIP1	protein_coding	protein_coding	ENST00000399599	4	28154

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.870	0.128	124739	0	11	124750	0.0000441

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.438	107	121	0.888	0.00000659	1315
Missense in Polyphen		27	41.557	0.6497		457
Synonymous	0.837	43	50.6	0.850	0.00000318	437
Loss of Function	2.39	0	6.67	0.00	2.81e-7	86

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000755	0.0000706
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as an important p53/TP53-apoptotic effector. Regulates TNF-alpha-mediated apoptosis in a p53/TP53-dependent manner. {ECO:0000269|PubMed:17599062}.

Recessive Scores

• pRec: 0.124

Intolerance Scores

• rvis_EVS: -0.23
• rvis_percentile_EVS: 36.86

Haploinsufficiency Scores

• pHI: 0.163
• hipred: N
• hipred_score: 0.287
• ghis: 0.551

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cdip1

Gene ontology

• Biological process: apoptotic process;tumor necrosis factor-mediated signaling pathway;intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator
• Cellular component: nucleus;cytoplasmic side of late endosome membrane;cytoplasmic side of lysosomal membrane
• Molecular function: molecular_function;protein binding;metal ion binding