CDIP1

Summary

CDIP1 (cell death inducing p53 target 1, HGNC:13234) is a protein-coding gene on chromosome 16p13.3, encoding Cell death-inducing p53-target protein 1 (Q9H305). Acts as an important p53/TP53-apoptotic effector.

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.

Source: NCBI Gene 29965 — automated summary from GO annotations (Alliance of Genome Resources).

At a glance

• GWAS associations: 9
• Clinical variants (ClinVar): 44 total
• GTEx eGene: eQTL in 38 tissues, sQTL in 37 (q < 0.05)
• Constraint (gnomAD): pLI 0.01 (LoF-tolerant), LOEUF 1.14 (unconstrained)
• MANE Select transcript: NM_013399

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:13234
Approved symbol	CDIP1
Name	cell death inducing p53 target 1
Location	16p13.3
Locus type	gene with protein product
Status	Approved
Aliases	CDIP, LITAFL
Ensembl gene	ENSG00000089486
Ensembl biotype	protein_coding
OMIM	610503
Entrez	29965

Gene structure

Transcript identifiers

Ensembl transcripts: 41 — 39 protein_coding, 1 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

MANE Select: ENST00000567695

Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 1: 4, TSL 2: 2, TSL 3: 2, TSL 4: 1, TSL 5: 5

ENST00000567695, ENST00000399599, ENST00000562334, ENST00000562579, ENST00000563186, ENST00000563332, ENST00000563507, ENST00000564828, ENST00000566234, ENST00000586728, ENST00000586768, ENST00000588381, ENST00000589159, ENST00000589890, ENST00000857432, ENST00000857433, ENST00000857434, ENST00000857435, ENST00000857436, ENST00000857437, ENST00000857438, ENST00000857439, ENST00000857440, ENST00000857441, ENST00000857442, ENST00000857443, ENST00000857444, ENST00000857445, ENST00000857446, ENST00000857447, ENST00000857448, ENST00000921885, ENST00000921886, ENST00000921887, ENST00000921888, ENST00000921889, ENST00000945079, ENST00000945083, ENST00001001586, ENST00001045266, ENST00001136834

RefSeq mRNA: 4 — MANE Select: NM_013399 NM_001199054, NM_001199055, NM_001199056, NM_013399

CCDS: CCDS42114, CCDS58419, CCDS58420

Canonical transcript exons

ENST00000567695 — 6 exons

Exon	Start	End
ENSE00000363280	4512791	4513064
ENSE00001145764	4514575	4514664
ENSE00002579466	4538702	4538773
ENSE00002582551	4510669	4512683
ENSE00003562425	4514046	4514144
ENSE00003628267	4513696	4513851

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 98.19.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 47.5596 / max 883.7407, expressed in 1686 samples.

Highest expression (Bgee): prefrontal cortex, frontal lobe, frontal cortex, primary visual cortex, dorsolateral prefrontal cortex.

Genetic regulation across tissues (GTEx eQTL / sQTL)

CDIP1 is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 38 tissues and its splicing (sQTL) in 37 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

showing 20 of 75 significant tissue × QTL associations:

Tissue	QTL	q-value	Slope	Lead variant
Cells Cultured fibroblasts	eqtl	1.8e-73	-0.67	16:4544670:C:T
Brain Cerebellum	eqtl	6.7e-66	-0.87	16:4510928:G:C
Brain Cerebellar Hemisphere	eqtl	1.2e-51	-0.77	16:4527089:A:G
Thyroid	eqtl	5.6e-49	+0.45	16:4523331:C:T
Muscle Skeletal	eqtl	5.0e-44	-0.35	16:4537788:A:G
Esophagus Muscularis	eqtl	1.8e-37	+0.50	16:4499617:G:A
Artery Tibial	eqtl	2.4e-30	+0.40	16:4523331:C:T
Nerve Tibial	eqtl	4.5e-29	-0.33	16:4544670:C:T
Colon Sigmoid	eqtl	1.9e-27	+0.44	16:4525161:C:T
Brain Cerebellum	sqtl	3.7e-25	+0.89	16:4494504:C:T
Muscle Skeletal	sqtl	1.5e-24	+0.57	16:4535882:AC:A
Colon Transverse	eqtl	1.1e-23	+0.32	16:4499225:C:G
Brain Cerebellar Hemisphere	sqtl	2.8e-23	-0.94	16:4528731:A:G
Nerve Tibial	sqtl	3.3e-22	-0.70	16:4494504:C:T
Esophagus Gastroesophageal Junction	eqtl	5.4e-22	+0.47	16:4499225:C:G
Esophagus Muscularis	sqtl	2.1e-20	+0.70	16:4533146:C:T
Lung	eqtl	2.9e-19	+0.29	16:4523331:C:T
Cells EBV-transformed lymphocytes	eqtl	2.6e-18	-0.64	16:4546113:A:G
Adipose Subcutaneous	sqtl	8.3e-17	-0.63	16:4527089:A:G
Artery Aorta	sqtl	3.5e-16	+0.66	16:4545268:G:A

FANTOM5 promoters

7 alternative TSS:

Promoter ID	TPM avg	Samples expressed
156100	38.5532	1683
156098	3.3489	861
156097	3.2425	589
156101	1.6100	774
156099	0.5876	381
156094	0.1910	79
156093	0.0264	8

Top tissues by expression

showing 100 of 134 tissues by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
prefrontal cortex	UBERON:0000451	98.19	gold quality
right frontal lobe	UBERON:0002810	98.16	gold quality
frontal cortex	UBERON:0001870	98.13	gold quality
primary visual cortex	UBERON:0002436	98.00	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	97.93	gold quality
Brodmann (1909) area 9	UBERON:0013540	97.90	gold quality
superior frontal gyrus	UBERON:0002661	97.88	gold quality
anterior cingulate cortex	UBERON:0009835	97.81	gold quality
cerebral cortex	UBERON:0000956	97.77	gold quality
nucleus accumbens	UBERON:0001882	97.73	gold quality
hypothalamus	UBERON:0001898	97.56	gold quality
putamen	UBERON:0001874	97.48	gold quality
caudate nucleus	UBERON:0001873	97.38	gold quality
right hemisphere of cerebellum	UBERON:0014890	97.37	gold quality
temporal lobe	UBERON:0001871	97.36	gold quality
amygdala	UBERON:0001876	97.35	gold quality
brain	UBERON:0000955	97.19	gold quality
cerebellum	UBERON:0002037	97.19	gold quality
cerebellar hemisphere	UBERON:0002245	97.19	gold quality
cerebellar cortex	UBERON:0002129	97.17	gold quality
Ammon’s horn	UBERON:0001954	97.12	gold quality
substantia nigra	UBERON:0002038	96.87	gold quality
apex of heart	UBERON:0002098	95.69	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	95.25	gold quality
adenohypophysis	UBERON:0002196	95.11	gold quality
pituitary gland	UBERON:0000007	94.90	gold quality
heart left ventricle	UBERON:0002084	93.91	gold quality
adult mammalian kidney	UBERON:0000082	93.37	gold quality
ventricular zone	UBERON:0003053	92.46	gold quality
ganglionic eminence	UBERON:0004023	92.45	gold quality
islet of Langerhans	UBERON:0000006	92.36	gold quality
hindlimb stylopod muscle	UBERON:0004252	92.00	gold quality
adrenal tissue	UBERON:0018303	91.92	gold quality
right adrenal gland cortex	UBERON:0035827	91.61	gold quality
kidney	UBERON:0002113	91.49	gold quality
cortical plate	UBERON:0005343	91.44	gold quality
left adrenal gland cortex	UBERON:0035825	91.37	gold quality
pancreas	UBERON:0001264	91.35	gold quality
heart	UBERON:0000948	91.27	gold quality
right adrenal gland	UBERON:0001233	91.27	gold quality
left adrenal gland	UBERON:0001234	91.24	gold quality
adrenal gland	UBERON:0002369	91.14	gold quality
right atrium auricular region	UBERON:0006631	91.08	gold quality
gastrocnemius	UBERON:0001388	90.96	gold quality
duodenum	UBERON:0002114	90.94	gold quality
body of pancreas	UBERON:0001150	90.61	gold quality
cortex of kidney	UBERON:0001225	90.59	gold quality
muscle of leg	UBERON:0001383	90.44	gold quality
granulocyte	CL:0000094	90.37	gold quality
skeletal muscle tissue	UBERON:0001134	90.34	gold quality
right lobe of liver	UBERON:0001114	90.11	gold quality
muscle tissue	UBERON:0002385	90.04	gold quality
metanephros cortex	UBERON:0010533	89.46	gold quality
left ovary	UBERON:0002119	89.45	gold quality
ovary	UBERON:0000992	89.44	gold quality
ascending aorta	UBERON:0001496	89.39	gold quality
thoracic aorta	UBERON:0001515	89.27	gold quality
body of uterus	UBERON:0009853	89.26	gold quality
stromal cell of endometrium	CL:0002255	89.23	gold quality
myometrium	UBERON:0001296	89.06	gold quality
right ovary	UBERON:0002118	89.04	gold quality
left uterine tube	UBERON:0001303	88.81	gold quality
multicellular organism	UBERON:0000468	88.78	gold quality
fundus of stomach	UBERON:0001160	88.78	gold quality
liver	UBERON:0002107	88.66	gold quality
leukocyte	CL:0000738	88.45	gold quality
descending thoracic aorta	UBERON:0002345	88.31	gold quality
monocyte	CL:0000576	88.23	gold quality
small intestine	UBERON:0002108	88.21	gold quality
lower esophagus muscularis layer	UBERON:0035833	88.12	gold quality
lower esophagus	UBERON:0013473	88.09	gold quality
smooth muscle tissue	UBERON:0001135	87.99	gold quality
left testis	UBERON:0004533	87.96	gold quality
tibial nerve	UBERON:0001323	87.87	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	87.69	gold quality
small intestine Peyer’s patch	UBERON:0003454	87.67	gold quality
testis	UBERON:0000473	87.58	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	87.56	gold quality
right lobe of thyroid gland	UBERON:0001119	87.56	gold quality
right testis	UBERON:0004534	87.46	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	87.42	gold quality
muscle layer of sigmoid colon	UBERON:0035805	87.36	gold quality
uterine cervix	UBERON:0000002	87.32	gold quality
left lobe of thyroid gland	UBERON:0001120	87.28	gold quality
endocervix	UBERON:0000458	87.27	gold quality
thyroid gland	UBERON:0002046	87.18	gold quality
ectocervix	UBERON:0012249	87.12	gold quality
prostate gland	UBERON:0002367	86.97	gold quality
body of stomach	UBERON:0001161	86.95	gold quality
popliteal artery	UBERON:0002250	86.83	gold quality
esophagus	UBERON:0001043	86.82	gold quality
tibial artery	UBERON:0007610	86.81	gold quality
blood	UBERON:0000178	86.80	gold quality
mucosa of stomach	UBERON:0001199	86.62	gold quality
urinary bladder	UBERON:0001255	86.26	gold quality
stomach	UBERON:0000945	86.11	gold quality
intestine	UBERON:0000160	85.80	gold quality
esophagus mucosa	UBERON:0002469	85.76	gold quality
fallopian tube	UBERON:0003889	85.73	gold quality
omental fat pad	UBERON:0010414	85.69	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.64

HPA expression

RNA tissue specificity: Tissue enhanced

showing 60 of 79 HPA tissues / cells by nTPM:

Tissue / cell	Axis	nTPM	Protein (IHC)
Frontal cortex	tissue	203.8
Caudate putamen	tissue	198.3
Postcentral gyrus	tissue	151.8
Cerebral cortex	tissue	149.5	medium
Somatosensory cortex	tissue	149.5
Motor cortex	tissue	146.0
Hippocampal formation	tissue	142.6
Occipital cortex	tissue	139.9
Prefrontal cortex	tissue	139.0
Thalamus	tissue	136.7
Pons	tissue	133.0
Temporal cortex	tissue	129.1
Retrosplenial and cingulate cortex	tissue	127.8
Insular cortex	tissue	124.8
Superior colliculi	tissue	122.2
Retrosplenial cortex	tissue	121.7
Entorhinal cortex	tissue	121.3
Hypothalamus	tissue	117.7
Midbrain	tissue	116.7
Medulla oblongata	tissue	111.2
Substantia nigra	tissue	109.3
Putamen	tissue	107.1
Locus coeruleus	tissue	106.9
Amygdala	tissue	105.4
Basal ganglia	tissue	105.1	medium
Ventral forebrain	tissue	103.0
Hippocampus	tissue	101.0	medium
Septum	tissue	99.9
Spinal cord	tissue	96.5
Periaqueductal gray	tissue	94.2
Nucleus accumbens	tissue	92.9
Cerebellum	tissue	92.4	medium
Corpus callosum	tissue	81.0
Olfactory bulb	tissue	61.9
Pituitary gland	tissue	59.9
Choroid plexus	tissue	32.0
Skeletal muscle	tissue	19.0	medium
Vagina	tissue	17.8	medium
Duodenum	tissue	13.6	medium
Ovary	tissue	11.8	medium
Small intestine	tissue	11.7	medium
Kidney	tissue	11.5	medium
Thymus	tissue	10.7
Seminal vesicle	tissue	10.3	low
Adipose tissue	tissue	10.1	low
Pancreas	tissue	10.0	medium
Heart muscle	tissue	9.9	medium
Endometrium 1	tissue	8.8	medium
Prostate	tissue	8.4	low
Cervix	tissue	8.2	medium
Adrenal gland	tissue	8.2	medium
Tongue	tissue	7.8
Gallbladder	tissue	7.4	medium
Parathyroid gland	tissue	6.7	medium
Liver	tissue	6.7	low
Skin 1	tissue	6.6	medium
Smooth muscle	tissue	6.6	medium
Retina	tissue	6.4
Fallopian tube	tissue	6.4	high
Spleen	tissue	6.3	not detected

Brain sub-regions (HPA Brain Atlas): detected in 192; highest nTPM — Precentral gyrus (162.1), Dorsal hippocampus (142.6), Postcentral gyrus, middle (139.3), Ventral hippocampus (138.4), Paracentral lobule, anterior (124.4).

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

Targeting CDIP1 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific).

showing 30 of 77 miRNAs:

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-4673	100.00	66.64	1490
HSA-MIR-6876-5P	100.00	67.68	2126
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-8485	100.00	77.57	4731
HSA-MIR-4476	100.00	68.18	2030
HSA-MIR-513A-5P	100.00	69.77	2465
HSA-MIR-34A-5P	99.99	71.21	1784
HSA-MIR-449A	99.99	71.05	1776
HSA-MIR-3667-3P	99.99	67.17	1636
HSA-MIR-27A-3P	99.98	72.13	2955
HSA-MIR-27B-3P	99.98	72.13	2955
HSA-MIR-9985	99.98	72.11	2939
HSA-MIR-4645-5P	99.98	65.81	1284
HSA-MIR-4715-3P	99.98	66.03	670
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-34C-5P	99.97	70.45	1577
HSA-MIR-449B-5P	99.97	70.26	1580
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-128-3P	99.95	71.17	2484
HSA-MIR-216A-3P	99.95	71.19	2505
HSA-MIR-4760-3P	99.93	70.50	2385
HSA-MIR-6721-5P	99.93	68.92	2981
HSA-MIR-3681-3P	99.88	70.46	2254
HSA-MIR-4492	99.87	68.25	3611
HSA-MIR-6715A-3P	99.83	68.05	1473
HSA-MIR-205-5P	99.81	70.05	1557
HSA-MIR-3934-3P	99.76	65.51	1351
HSA-MIR-6764-5P	99.75	67.89	2304

Functional genomics

gnomAD constraint: pLI 0.00687, LOEUF 1.14, missense Z -0.0734 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD

Regional missense constraint (gnomAD RMC): no regional variation along ENST00000567695 — one region, missense o/e 0.95.

Literature-anchored findings (GeneRIF, showing 6)

• These findings support a novel p53 –> CDIP –> TNF-alpha apoptotic pathway that directs apoptosis after exposure of cells to genotoxic stress. (PMID:17599062)
• CDIP expression correlates with sensitivity of cancer cells with TNFalpha, and CDIP seems to be a regulator of the p53-mediated death versus survival response of cells to TNFalpha. (PMID:22549949)
• Study conclude that LITAF is a monotopic membrane protein whose membrane integration is stabilised by a zinc finger. The related human protein, CDIP1 (cell death involved p53 target 1), displays identical membrane topology, suggesting that this mode of membrane integration is conserved in LITAF family proteins. (PMID:27582497)
• The Novel ALG-2 Target Protein CDIP1 Promotes Cell Death by Interacting with ESCRT-I and VAPA/B. (PMID:33503978)
• Role of ELK1 in regulating colorectal cancer progression: miR-31-5p/CDIP1 axis in CRC pathogenesis. (PMID:37547727)
• Cytoprotective Role of Autophagy in CDIP1 Expression-Induced Apoptosis in MCF-7 Breast Cancer Cells. (PMID:38928226)

Cross-species orthologs

14 orthologs

Organism	Symbol	Gene ID
danio_rerio	cdip1	ENSDARG00000076118
mus_musculus	Cdip1	ENSMUSG00000004071
rattus_norvegicus	Cdip1	ENSRNOG00000003328
drosophila_melanogaster	CG12645	FBGN0030181
drosophila_melanogaster	CG13510	FBGN0034758
drosophila_melanogaster	CG4250	FBGN0034761
drosophila_melanogaster	CG13516	FBGN0040658
drosophila_melanogaster	CG30269	FBGN0050269
drosophila_melanogaster	CG30273	FBGN0050273
caenorhabditis_elegans		WBGENE00012548
caenorhabditis_elegans		WBGENE00012748
caenorhabditis_elegans		WBGENE00017513
caenorhabditis_elegans		WBGENE00021253
caenorhabditis_elegans	Y87G2A.19	WBGENE00044260

Paralogs (1): LITAF (ENSG00000189067)

Mouse-model phenotypes

Observed phenotypes of the mouse ortholog (MGI:1913876) from MGI (Alliance of Genome Resources) — knockout/mutant phenotypes, ranked by annotation count. 5 distinct phenotype terms.

Mouse phenotype (MP)	Records
hyperactivity	1
abnormal behavior	1
decreased apoptosis	1
preweaning lethality, complete penetrance	1
decreased thigmotaxis	1

Additional cross-species homologs

Sequence homologs in species beyond Ensembl Compara’s model organisms, by Diamond local protein alignment (% sequence identity; best hit per species). Lower-identity rows are more distant homologs. The matched accessions’ gene symbols aren’t in biobtree yet, so each row shows the UniProt accession.

Organism	UniProt	Identity	Method
Bos taurus	Q58D45	88.5%	Diamond
Xenopus tropicalis	Q5BJ83	75.4%	Diamond
Xenopus laevis	Q8AVW3	75.4%	Diamond
Gallus gallus	Q8QGW7	64.2%	Diamond
Dictyostelium discoideum	Q54HX8	53.7%	Diamond
Frog virus 3 (isolate Goorha)	Q6GZQ0	40.6%	Diamond

Genomic neighbors (locus context)

Genes flanking this one on the chromosome (NCBI/Entrez gene neighborhood). Positional context only — some neighbors share regulatory elements (bidirectional promoters, antisense/overlapping transcripts), but chromosomal adjacency is not itself a functional relationship (see Interactions for that).

Symbol	Type	Entrez
UBALD1	protein-coding	124402
MGRN1	protein-coding	23295
HMOX2	protein-coding	3163
C16orf96	protein-coding	342346
MIR6769A	ncRNA	102466731
NMRAL1	protein-coding	57407
DNAJA3	protein-coding	9093

Protein

Protein identifiers

Cell death-inducing p53-target protein 1 — Q9H305 (reviewed: Q9H305)

Alternative names: Cell death involved p53-target, Cell death-inducing protein, LITAF-like protein, Lipopolysaccharide-induced tumor necrosis factor-alpha-like protein, Transmembrane protein I1

All UniProt accessions (9): Q9H305, H3BRY7, H3BTN7, H3BTX4, K7EK15, K7ELR4, K7EM67, K7ENR4, K7ESA8

UniProt curated annotations — full annotation on UniProt →

Function. Acts as an important p53/TP53-apoptotic effector. Regulates TNF-mediated apoptosis in a p53/TP53-dependent manner.

Subcellular location. Late endosome membrane. Lysosome membrane.

Tissue specificity. Highly expressed in brain. Expressed at lower level in heart, skeletal muscle, kidney, pancreas and liver. Weakly or not expressed in placenta and lung.

Domain organisation. The LITAF domain is stabilized by a bound zinc ion. The LITAF domain contains an amphipathic helix that mediates interaction with lipid membranes.

Induction. Up-regulated by p53/TP53.

Miscellaneous. May be due to competing acceptor splice site.

Similarity. Belongs to the CDIP1/LITAF family.

Isoforms (3)

UniProt ID	Names	Canonical?
Q9H305-1	1	yes
Q9H305-2	2
Q9H305-3	3

RefSeq proteins (4): NP_001185983, NP_001185984, NP_001185985, NP_037531* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR006629	LITAF	Domain
IPR037519	LITAF_fam	Family

Pfam: PF10601

UniProt features (13 total): binding site 4, splice variant 2, region of interest 2, compositionally biased region 2, chain 1, domain 1, sequence conflict 1

Structure

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9H305-F1	55.37	0.00

Human Protein Atlas

Protein class: Predicted membrane proteins, Predicted intracellular proteins

Protein evidence: Evidence at protein level

Subcellular location (HPA, imaging): centrosome; nucleoplasm

Antibody reliability (HPA): IH approved · IF supported

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Ligand- & substrate-binding residues (4)

Position	Role
142	Zn(2+)
145	Zn(2+)
194	Zn(2+)
197	Zn(2+)

Function

Pathways and Gene Ontology

Reactome pathways

0 curated (TAS) of 0; 0 disease pathways. Curated-first; evidence = TAS (manually curated) vs IEA (electronic inference).

MSigDB gene sets: 162 (showing top): GGGACCA_MIR133A_MIR133B, GOBP_INTRINSIC_APOPTOTIC_SIGNALING_PATHWAY_IN_RESPONSE_TO_DNA_DAMAGE_BY_P53_CLASS_MEDIATOR, GOCC_VACUOLAR_MEMBRANE, TTTGTAG_MIR520D, LINDGREN_BLADDER_CANCER_CLUSTER_3_DN, LUCAS_HNF4A_TARGETS_UP, GOCC_MICROTUBULE_ORGANIZING_CENTER, SHEDDEN_LUNG_CANCER_GOOD_SURVIVAL_A5, GOBP_APOPTOTIC_SIGNALING_PATHWAY, BLALOCK_ALZHEIMERS_DISEASE_UP, GOCC_CENTROSOME, GOBP_INTRINSIC_APOPTOTIC_SIGNALING_PATHWAY_IN_RESPONSE_TO_DNA_DAMAGE, SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_DN, GOBP_DNA_DAMAGE_RESPONSE, GOBP_INTRINSIC_APOPTOTIC_SIGNALING_PATHWAY

GO Biological Process (2): intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771), apoptotic process (GO:0006915)

GO Molecular Function (3): zinc ion binding (GO:0008270), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (7): nucleus (GO:0005634), nucleoplasm (GO:0005654), centrosome (GO:0005813), cytoplasmic side of late endosome membrane (GO:0098560), cytoplasmic side of lysosomal membrane (GO:0098574), lysosomal membrane (GO:0005765), late endosome membrane (GO:0031902)

GO top-level categories

21 GO namespaces:

Category	Terms
intrinsic apoptotic signaling pathway in response to DNA damage	1
intrinsic apoptotic signaling pathway by p53 class mediator	1
programmed cell death	1
apoptotic signaling pathway	1
execution phase of apoptosis	1
transition metal ion binding	1
binding	1
cation binding	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
cellular anatomical structure	1
centriole	1
microtubule organizing center	1
cytoplasmic side of endosome membrane	1
late endosome membrane	1
lysosomal membrane	1
cytoplasmic side of membrane	1
lysosome	1
lytic vacuole membrane	1
late endosome	1
endosome membrane	1

Experimentally-supported GO annotations

GO terms backed by direct experimental evidence (ECO experimental codes) — 6 of 12 annotations. The rest are phylogenetic / computational / electronic (IEA).

6 experimentally-supported GO terms:

GO term	NS	Evidence
intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator	BP	mutant phenotype
centrosome	CC	direct assay
cytoplasmic side of late endosome membrane	CC	direct assay
cytoplasmic side of lysosomal membrane	CC	direct assay
nucleoplasm	CC	direct assay
nucleus	CC	direct assay

Protein interactions and networks

STRING

showing 16 of 418 interactions by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CDIP1	ASPHD1	Q5U4P2	464
CDIP1	UQCC5	Q8WVI0	438
CDIP1	OGFOD2	Q6N063	436
CDIP1	BCAP31	P51572	435
CDIP1	UBE2O	Q9C0C9	429
CDIP1	MTFP1	Q9UDX5	388
CDIP1	OR2C1	O95371	371
CDIP1	RAB11FIP5	Q9BXF6	370
CDIP1	PACSIN2	Q9UNF0	370
CDIP1	SRP68	Q9UHB9	370
CDIP1	DDX47	Q9H0S4	370
CDIP1	RAB11FIP2	Q7L804	370
CDIP1	CARHSP1	Q9Y2V2	370
CDIP1	SMYD4	Q8IYR2	367
CDIP1	SMDT1	Q9H4I9	366
CDIP1	IGFALS	P35858	366

IntAct

Human interaction partners of CDIP1 in IntAct, one row per partner (best MIscore; records = supporting IntAct interaction records).

16 partners by confidence:

Partner	Interaction type	MIscore	Records
TNIP1	physical association	0.670	4
DESI1	physical association	0.600	4
DCUN1D1	physical association	0.560	3
EPN2	physical association	0.560	3
LAT	physical association	0.560	3
OTUB2	physical association	0.560	3
OTUD7B	physical association	0.560	3
TOLLIP	physical association	0.560	3
UBB	physical association	0.560	3
UBC	physical association	0.560	3
UBQLN1	physical association	0.560	3
UBQLN2	physical association	0.560	3
NEDD4	direct interaction	0.440	1
YAP1	direct interaction	0.440	1
ATXN1	physical association	0.370	1
CCR2	physical association	0.370	1

BioGRID (20 interactions; top human partners by supporting records): TNIP1 (Two-hybrid; 2 records), ATXN1 (Two-hybrid), CCR2 (Two-hybrid), DCUN1D1 (Two-hybrid), DESI1 (Two-hybrid), EPN2 (Two-hybrid), LAT (Two-hybrid), LITAF (Synthetic Rescue), NEDD4 (Protein-peptide), OTUB2 (Two-hybrid), OTUD7B (Two-hybrid), TOLLIP (Two-hybrid), TRIM25 (Affinity Capture-RNA), TRIM71 (Affinity Capture-RNA), UBB (Two-hybrid)

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 16 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Ovarian tumor domain proteases	5	99.5×	2e-07
Cargo recognition for clathrin-mediated endocytosis	5	37.4×	1e-05

Disease & clinical

Genetic variants

Variant evidence for CDIP1: 44 ClinVar records (0 pathogenic / likely pathogenic); 9 GWAS associations.

ClinVar

44 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	32
Likely benign	4
Benign	0

SpliceAI

Top 10 splice-impact sites by Δscore (adjacent positions with the same effect merged into one range; 33 predictions of 791):

Position(s)	Effect	Δscore	Sites
16:4512816	donor_gain	1.0000
16:4513852–4513853	acceptor_loss	1.0000	6
16:4514151	acceptor_gain	1.0000
16:4514573	donor_loss	1.0000	2
16:4512684–4512685	acceptor_loss	0.9900	5
16:4512691	acceptor_gain	0.9900
16:4512789–4512790	donor_loss	0.9900	5
16:4513694–4513695	donor_loss	0.9900	6
16:4513858	acceptor_gain	0.9900
16:4514044–4514045	donor_loss	0.9900	5

HPA cancer prognostics

RNA cancer specificity: Low cancer specificity

Human Protein Atlas survival analysis — favorable = higher expression predicts better survival.

3 prognostic cancer types:

Cancer	Prognostic	p-value
Kidney Renal Clear Cell Carcinoma (TCGA)	favorable	2.61e-05
Pancreatic Adenocarcinoma (TCGA)	favorable	5.4e-05
Stomach Adenocarcinoma (TCGA)	unfavorable	0.000485

Disease associations

OMIM: gene MIM:610503 | disease phenotypes:

GWAS associations

9 associations:

Study	Trait	p-value
GCST90020024_938	A body shape index	3e-10
GCST90002382_360	Eosinophil percentage of white cells	7e-10
GCST004946_131	Schizophrenia	5e-9
GCST90020027_972	Waist-hip index	2e-8
GCST90020025_1835	Waist-to-hip ratio adjusted for BMI	3e-8
GCST90020025_1836	Waist-to-hip ratio adjusted for BMI	3e-8
GCST012227_149	Hip circumference adjusted for BMI	4e-8
GCST012490_151	Femur bone mineral density x serum urate levels interaction	4e-8
GCST90020027_973	Waist-hip index	4e-8

EFO canonical traits (from GWAS)

5 canonical traits:

EFO ID	Trait name
EFO:0008039	BMI-adjusted hip circumference
EFO:0004531	urate measurement
EFO:0007991	eosinophil percentage of leukocytes
EFO:0007789	BMI-adjusted waist circumference
EFO:0007788	BMI-adjusted waist-hip ratio

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (CPIC guideline: no)

CTD chemical–gene interactions

34 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, decreases methylation, increases expression, increases methylation	4
Aflatoxin B1	affects expression, increases expression, increases methylation	4
FR900359	decreases phosphorylation	1
dicrotophos	increases expression	1
propionaldehyde	increases expression	1
sodium arsenite	increases expression	1
butyraldehyde	increases expression	1
pentanal	increases expression	1
di-n-butylphosphoric acid	affects expression	1
nutlin 3	affects cotreatment, increases expression	1
abrine	increases expression	1
jinfukang	affects cotreatment, increases expression	1
prothioconazole	decreases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Acetaminophen	increases expression	1
Air Pollutants	decreases expression, increases abundance	1
Aldehydes	increases expression	1
Atrazine	decreases expression	1
Camptothecin	increases expression	1
Cisplatin	affects cotreatment, increases expression	1
Dactinomycin	increases expression, affects cotreatment	1
Dimethyl Sulfoxide	decreases expression	1
Doxorubicin	increases expression	1
Ethyl Methanesulfonate	increases expression	1
Formaldehyde	increases expression	1
Methyl Methanesulfonate	increases expression	1
Plant Extracts	affects cotreatment, decreases expression	1
Quercetin	increases expression	1
Silicon Dioxide	increases expression	1
Smoke	decreases expression, increases abundance	1

Clinical trials (associated diseases)

Via MONDO — disease-level, not drug-specific.

12 trials:

NCT	Phase	Status	Title
NCT03414970	Phase 3	ACTIVE_NOT_RECRUITING	Hypofractionated Radiation Therapy After Mastectomy in Preventing Recurrence in Patients With Stage IIa-IIIa Breast Cancer
NCT00461344	Phase 2	TERMINATED	Docetaxel + Doxorubicin as Neoadjuvant Chemotherapy in Patients With Breast Cancer
NCT07499999	Phase 2	NOT_YET_RECRUITING	Randomized Double-Blind Phase II Trial of Baby Exemestane Versus Baby Tamoxifen in Post-Menopausal Women at High Risk for Breast Cancer
NCT00637364	Phase 1/2	SUSPENDED	High Intensity Focused Ultrasound Tumor Treatment for Pancreatic Cancer Pain
NCT02779855	Phase 1/2	COMPLETED	Talimogene Laherparepvec in Combination With Neoadjuvant Chemotherapy in Triple Negative Breast Cancer
NCT01753908	Early Phase 1	COMPLETED	Broccoli Sprout Extract in Treating Patients With Breast Cancer
NCT01796041	Early Phase 1	COMPLETED	Intraoperative Imaging of Breast Cancer With Indocyanine Green
NCT07628634	Early Phase 1	RECRUITING	Feasibility Study on the Effect of a Methionine-Reduced Diet on Serum Levels in Pts w/ Solid Tumors
NCT01208974	Not specified	COMPLETED	Nipple-Areola Complex (NAC) Irradiation After Nipple-Sparing Mastectomy and Reconstruction
NCT01875198	Not specified	TERMINATED	Oncologic Impact of Splenectomy-omitting Radical Pancreatectomy in Well-selected Left-sided Pancreatic Cancer
NCT03543397	Not specified	UNKNOWN	MRI in Ductal Carcinoma in Situ (DCIS)
NCT03834532	Not specified	COMPLETED	Living Well After Breast Surgery