CDIP1

protein-coding

cell death inducing p53 target 1

Gene summary

Predicted to enable zinc ion binding activity. Acts upstream of or within intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator. Located in bounding membrane of organelle; centrosome; and nucleoplasm. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

C16orf5

MANE transcript

NM_013399.3

Inheritance

—

ClinVar variants

U:36B:3

Top phenotype

EBV-positive nodal T- and NK-cell lymphoma

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr16:4,510,669-4,538,828

External References & Databases

Ensembl (ENSG00000089486)

Transcript & Mutation Effects

hg38 • Region Span ~28.2 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 CDIP1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 32

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_013399.3. 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	1 clinvar		2
missense			33 clinvar	2 clinvar		35
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	36	3	0	39

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 75 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_013399.3	RefSeq	NP_037531.2	4	MANE Select
ENST00000567695.6	Ensembl	ENSP00000457877.1	4	MANE Select
NM_001199054.2	RefSeq	NP_001185983.1	4	Standard
NM_001199055.2	RefSeq	NP_001185984.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

apoptotic process
tumor necrosis factor-mediated signaling pathway
intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator

Molecular Function

molecular_function
protein binding
metal ion binding

Cellular Component

nucleus
cytoplasmic side of late endosome membrane
cytoplasmic side of lysosomal membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000399599
Coding exons: 4
Length: 28154
Individuals with no LoFs: 124739
Homozygous LoFs: 0
Heterozygous LoFs: 11
Defined: 124750
p: 0.0000441

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.438	107	121	0.888	0.00000659	1315
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000065	0.000065	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000075	0.000071	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N

Gene Damage Prediction

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