ATF7IP2

Summary

ATF7IP2 (activating transcription factor 7 interacting protein 2, HGNC:20397) is a protein-coding gene on chromosome 16p13.2-p13.13, encoding Activating transcription factor 7-interacting protein 2 (Q5U623). Recruiter that couples transcriptional factors to general transcription apparatus and thereby modulates transcription regulation and chromatin formation.

Predicted to enable transcription coregulator activity. Predicted to be involved in regulation of DNA-templated transcription. Predicted to be part of transcription regulator complex. Predicted to be active in nucleus.

Source: NCBI Gene 80063 — automated summary from GO annotations (Alliance of Genome Resources).

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 160 total — 1 pathogenic
• GTEx eGene: eQTL in 33 tissues, sQTL in 5 (q < 0.05)
• Constraint (gnomAD): pLI 0.00 (LoF-tolerant), LOEUF 0.91 (unconstrained)
• MANE Select transcript: NM_001393719
• Notable: 160 clinical variants but no curated precision-oncology (CIViC) evidence yet

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:20397
Approved symbol	ATF7IP2
Name	activating transcription factor 7 interacting protein 2
Location	16p13.2-p13.13
Locus type	gene with protein product
Status	Approved
Aliases	FLJ12668, MCAF2
Ensembl gene	ENSG00000166669
Ensembl biotype	protein_coding
OMIM	613645
Entrez	80063

Gene structure

Transcript identifiers

Ensembl transcripts: 35 — 21 protein_coding, 7 nonsense_mediated_decay, 5 retained_intron, 2 protein_coding_CDS_not_defined

MANE Select: ENST00000562102

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

ENST00000562102, ENST00000324570, ENST00000356427, ENST00000396559, ENST00000396560, ENST00000535850, ENST00000543967, ENST00000561932, ENST00000562396, ENST00000562527, ENST00000564797, ENST00000565450, ENST00000565616, ENST00000566316, ENST00000568027, ENST00000569900, ENST00000569939, ENST00000570163, ENST00000876243, ENST00000876244, ENST00000876245, ENST00000876246, ENST00000876247, ENST00000914621, ENST00000914622, ENST00000914623, ENST00000914624, ENST00000950976, ENST00000975099, ENST00000975100, ENST00000975101, ENST00001028037, ENST00001028038, ENST00001120896, ENST00001136672

RefSeq mRNA: 4 — MANE Select: NM_001393719 NM_001256160, NM_001352120, NM_001393719, NM_024997

CCDS: CCDS10540, CCDS58422

Canonical transcript exons

ENST00000562102 — 14 exons

Exon	Start	End
ENSE00001203767	10438101	10438235
ENSE00001286005	10433525	10433649
ENSE00001322159	10457372	10457529
ENSE00001329066	10440364	10440462
ENSE00001525464	10430611	10431455
ENSE00001525465	10428868	10429016
ENSE00001525466	10386061	10386122
ENSE00001732210	10419581	10419623
ENSE00002595942	10414574	10414612
ENSE00003475249	10473923	10473989
ENSE00003495711	10473479	10473534
ENSE00003555489	10472110	10472183
ENSE00003621488	10480879	10480964
ENSE00003693025	10481836	10483638

Expression profiles

Bgee: expression breadth ubiquitous, 254 present calls, max score 97.12.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 16.7486 / max 326.4104, expressed in 1474 samples.

Highest expression (Bgee): testis, adrenal gland cortex, adrenal gland, corpus epididymis, lobe of liver.

Genetic regulation across tissues (GTEx eQTL / sQTL)

ATF7IP2 is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 33 tissues and its splicing (sQTL) in 5 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

showing 20 of 38 significant tissue × QTL associations:

Tissue	QTL	q-value	Slope	Lead variant
Testis	sqtl	1.4e-50	+1.11	16:10473169:A:G
Skin Sun Exposed Lower leg	eqtl	9.0e-49	-0.79	16:10373326:T:C
Adipose Subcutaneous	eqtl	9.6e-42	+0.50	16:10373073:G:A
Skin Not Sun Exposed Suprapubic	eqtl	9.3e-37	-0.64	16:10373326:T:C
Esophagus Mucosa	eqtl	1.4e-26	-0.62	16:10386357:A:G
Adrenal Gland	sqtl	5.7e-23	+1.00	16:10473169:A:G
Colon Transverse	eqtl	8.4e-21	-0.62	16:10367886:C:T
Nerve Tibial	eqtl	6.6e-20	-0.45	16:10386357:A:G
Esophagus Muscularis	eqtl	1.0e-17	-0.48	16:10386357:A:G
Artery Aorta	eqtl	1.2e-17	+0.52	16:10490454:T:G
Pancreas	sqtl	1.3e-16	+0.88	16:10473169:A:G
Thyroid	eqtl	3.9e-16	-0.39	16:10386357:A:G
Pancreas	eqtl	1.9e-15	+0.48	16:10404948:A:G
Esophagus Gastroesophageal Junction	eqtl	3.4e-15	-0.48	16:10446827:C:T
Breast Mammary Tissue	eqtl	2.4e-13	-0.50	16:10386357:A:G
Muscle Skeletal	eqtl	4.3e-12	-0.42	16:10386357:A:G
Liver	sqtl	1.8e-11	+1.07	16:10474374:G:C
Cells Cultured fibroblasts	eqtl	1.4e-09	+0.37	16:10368626:C:CTTTTG
Brain Frontal Cortex BA9	eqtl	1.4e-08	-0.30	16:10484245:C:CAA
Artery Tibial	eqtl	3.2e-08	+0.48	16:10489946:G:A

FANTOM5 promoters

2 alternative TSS:

Promoter ID	TPM avg	Samples expressed
152699	15.4324	1433
152698	1.3163	589

Top tissues by expression

showing 100 of 285 tissues by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
right testis	UBERON:0004534	97.12	gold quality
left testis	UBERON:0004533	97.02	gold quality
testis	UBERON:0000473	95.53	gold quality
left adrenal gland cortex	UBERON:0035825	94.75	gold quality
left adrenal gland	UBERON:0001234	94.74	gold quality
right adrenal gland	UBERON:0001233	94.63	gold quality
corpus epididymis	UBERON:0004359	94.15	gold quality
right lobe of liver	UBERON:0001114	94.08	gold quality
right adrenal gland cortex	UBERON:0035827	93.97	gold quality
body of pancreas	UBERON:0001150	92.97	gold quality
adrenal cortex	UBERON:0001235	92.87	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	92.71	gold quality
adrenal gland	UBERON:0002369	92.33	gold quality
sperm	CL:0000019	91.14	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	91.01	gold quality
heart left ventricle	UBERON:0002084	90.49	gold quality
male germ cell	CL:0000015	90.27	gold quality
cardiac ventricle	UBERON:0002082	90.02	gold quality
apex of heart	UBERON:0002098	89.88	gold quality
liver	UBERON:0002107	89.43	gold quality
right atrium auricular region	UBERON:0006631	88.94	gold quality
oocyte	CL:0000023	88.92	gold quality
pancreas	UBERON:0001264	88.64	gold quality
heart	UBERON:0000948	88.01	gold quality
bronchial epithelial cell	CL:0002328	87.99	gold quality
right uterine tube	UBERON:0001302	87.59	gold quality
secondary oocyte	CL:0000655	87.58	gold quality
cardiac atrium	UBERON:0002081	87.48	gold quality
epithelium of bronchus	UBERON:0002031	86.79	gold quality
body of stomach	UBERON:0001161	86.39	gold quality
bronchus	UBERON:0002185	86.10	gold quality
epithelium of nasopharynx	UBERON:0001951	85.78	gold quality
stomach	UBERON:0000945	85.55	gold quality
granulocyte	CL:0000094	85.51	gold quality
germinal epithelium of ovary	UBERON:0001304	85.28	gold quality
spleen	UBERON:0002106	85.22	gold quality
colonic epithelium	UBERON:0000397	85.16	gold quality
lymph node	UBERON:0000029	84.84	gold quality
leukocyte	CL:0000738	84.39	gold quality
bone marrow cell	CL:0002092	84.37	gold quality
monocyte	CL:0000576	84.34	gold quality
right lobe of thyroid gland	UBERON:0001119	84.30	gold quality
mononuclear cell	CL:0000842	84.27	gold quality
urinary bladder	UBERON:0001255	83.84	gold quality
left lobe of thyroid gland	UBERON:0001120	83.48	gold quality
thyroid gland	UBERON:0002046	83.44	gold quality
adrenal tissue	UBERON:0018303	83.38	gold quality
caput epididymis	UBERON:0004358	82.94	gold quality
islet of Langerhans	UBERON:0000006	82.88	gold quality
myocardium	UBERON:0002349	82.77	gold quality
tonsil	UBERON:0002372	82.64	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	82.61	gold quality
metanephros cortex	UBERON:0010533	82.49	gold quality
vermiform appendix	UBERON:0001154	82.38	gold quality
bone marrow	UBERON:0002371	82.37	gold quality
anterior cingulate cortex	UBERON:0009835	82.25	gold quality
left ventricle myocardium	UBERON:0006566	82.23	gold quality
cingulate cortex	UBERON:0003027	82.19	gold quality
left uterine tube	UBERON:0001303	82.01	gold quality
small intestine Peyer’s patch	UBERON:0003454	81.99	gold quality
adenohypophysis	UBERON:0002196	81.57	gold quality
adult organism	UBERON:0007023	81.34	gold quality
heart right ventricle	UBERON:0002080	81.27	gold quality
blood	UBERON:0000178	81.00	gold quality
amygdala	UBERON:0001876	80.97	gold quality
muscle layer of sigmoid colon	UBERON:0035805	80.74	gold quality
mucosa of stomach	UBERON:0001199	80.63	gold quality
prefrontal cortex	UBERON:0000451	80.61	gold quality
Brodmann (1909) area 9	UBERON:0013540	80.56	gold quality
right frontal lobe	UBERON:0002810	80.52	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	80.50	gold quality
small intestine	UBERON:0002108	80.43	gold quality
upper lobe of left lung	UBERON:0008952	80.39	gold quality
mucosa of urinary bladder	UBERON:0001259	80.38	gold quality
right lung	UBERON:0002167	80.34	gold quality
right coronary artery	UBERON:0001625	80.28	gold quality
ascending aorta	UBERON:0001496	80.13	gold quality
thoracic aorta	UBERON:0001515	79.99	gold quality
fundus of stomach	UBERON:0001160	79.98	gold quality
pituitary gland	UBERON:0000007	79.95	gold quality
mucosa of transverse colon	UBERON:0004991	79.95	gold quality
omental fat pad	UBERON:0010414	79.93	gold quality
caecum	UBERON:0001153	79.89	gold quality
peritoneum	UBERON:0002358	79.89	gold quality
nasal cavity mucosa	UBERON:0001826	79.74	gold quality
buccal mucosa cell	CL:0002336	79.65	gold quality
calcaneal tendon	UBERON:0003701	79.62	gold quality
upper lobe of lung	UBERON:0008948	79.50	gold quality
adipose tissue of abdominal region	UBERON:0007808	79.34	gold quality
ovary	UBERON:0000992	79.29	gold quality
middle temporal gyrus	UBERON:0002771	79.13	gold quality
smooth muscle tissue	UBERON:0001135	79.08	gold quality
tibia	UBERON:0000979	79.00	gold quality
caudate nucleus	UBERON:0001873	78.99	gold quality
fallopian tube	UBERON:0003889	78.94	gold quality
skin of abdomen	UBERON:0001416	78.90	gold quality
nucleus accumbens	UBERON:0001882	78.90	gold quality
adult mammalian kidney	UBERON:0000082	78.89	gold quality
putamen	UBERON:0001874	78.85	gold quality
descending thoracic aorta	UBERON:0002345	78.85	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	8.73
E-MTAB-6379	no	2166.60

HPA expression

RNA tissue specificity: Tissue enhanced

showing 60 of 77 HPA tissues / cells by nTPM:

Tissue / cell	Axis	nTPM	Protein (IHC)
Testis	tissue	16.7	high
Thymus	tissue	8.5
Liver	tissue	8.0	not detected
Tonsil	tissue	6.9	medium
Lymph node	tissue	6.7	medium
Hippocampus	tissue	6.2	low
Nucleus accumbens	tissue	5.4
Pancreas	tissue	5.3	not detected
Postcentral gyrus	tissue	5.3
Stomach 1	tissue	5.2	low
Choroid plexus	tissue	5.1
Adrenal gland	tissue	5.1	medium
Heart muscle	tissue	4.8	not detected
Bone marrow	tissue	4.5	low
Cerebral cortex	tissue	4.4	medium
Occipital cortex	tissue	4.4
Locus coeruleus	tissue	4.3
Fallopian tube	tissue	4.2	medium
Retina	tissue	4.1
Spleen	tissue	4.1	medium
Urinary bladder	tissue	4.0	medium
Somatosensory cortex	tissue	3.6
Appendix	tissue	3.5	medium
Epididymis	tissue	3.4	low
Retrosplenial and cingulate cortex	tissue	3.4
Thyroid gland	tissue	3.2	medium
Hippocampal formation	tissue	3.1
Entorhinal cortex	tissue	3.1
Prefrontal cortex	tissue	2.9
Motor cortex	tissue	2.8
Placenta	tissue	2.8	low
Duodenum	tissue	2.8	low
Cervix	tissue	2.7	low
Skin 1	tissue	2.6	low
Temporal cortex	tissue	2.5
Insular cortex	tissue	2.2
Ovary	tissue	2.0	not detected
Kidney	tissue	2.0	medium
Rectum	tissue	1.8	low
Small intestine	tissue	1.8	low
Retrosplenial cortex	tissue	1.8
Smooth muscle	tissue	1.6	low
Colon	tissue	1.6	low
Seminal vesicle	tissue	1.5	low
Adipose tissue	tissue	1.5	not detected
Skeletal muscle	tissue	1.5	low
Breast	tissue	1.4	low
Esophagus	tissue	1.4	low
Superior colliculi	tissue	1.4
Lung	tissue	1.4	low
Prostate	tissue	1.3	not detected
Endometrium 1	tissue	1.2	not detected
Pituitary gland	tissue	1.1
Gallbladder	tissue	1.1	low
Vagina	tissue	1.0	low
Corpus callosum	tissue	0.9
Amygdala	tissue	0.8
Thalamus	tissue	0.7
Tongue	tissue	0.6
Salivary gland	tissue	0.5	low

Brain sub-regions (HPA Brain Atlas): detected in 190; highest nTPM — Hippocampus, CA1 (8.4), Hippocampus, CA3 (8.2), Somatosensory cortex, postcentral gyrus, ventral (white matter) (8.0), Basal amygdala (7.6), Corticomedial amygdala (7.2).

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

Targeting ATF7IP2 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific).

showing 30 of 63 miRNAs:

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-4533	100.00	69.48	2758
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-19A-3P	99.98	75.33	2762
HSA-MIR-19B-3P	99.98	75.44	2754
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-545-3P	99.95	70.74	2783
HSA-MIR-7-1-3P	99.91	71.53	4384
HSA-MIR-7-2-3P	99.91	71.40	4394
HSA-MIR-9902	99.89	69.15	2250
HSA-MIR-137-3P	99.87	74.74	2401
HSA-MIR-5010-3P	99.83	70.60	2357
HSA-MIR-4307	99.82	70.45	3374
HSA-MIR-320A-3P	99.77	69.73	2107
HSA-MIR-320B	99.77	69.73	2107
HSA-MIR-320C	99.77	69.73	2107
HSA-MIR-320D	99.77	69.73	2107
HSA-MIR-4429	99.77	69.62	2111
HSA-MIR-4517	99.76	69.19	1867
HSA-MIR-519A-3P	99.67	71.67	1868
HSA-MIR-519B-3P	99.67	71.67	1868
HSA-MIR-519C-3P	99.67	71.67	1870
HSA-MIR-5093	99.67	69.26	2291
HSA-MIR-6762-3P	99.66	66.94	1188
HSA-MIR-7152-5P	99.60	69.33	2094

Functional genomics

gnomAD constraint: pLI 8.91e-06, LOEUF 0.909, missense Z -0.891 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD

Regional missense constraint (gnomAD RMC): no regional variation along ENST00000562102 — one region, missense o/e 1.19.

Literature-anchored findings (GeneRIF, showing 1)

• These data suggest that MBD1.MCAF1.SETDB1 complex facilitates the formation of heterochromatic domains, emphasizing the role of MCAF/AM family proteins in epigenetic control, and describe a new family member, MCAF2 (ATF7IP2). (PMID:15691849)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	atf7ip2	ENSDARG00000089698
mus_musculus	Atf7ip2	ENSMUSG00000039200
rattus_norvegicus	Atf7ip2	ENSRNOG00000025522
drosophila_melanogaster	wde	FBGN0027499

Paralogs (1): ATF7IP (ENSG00000171681)

Mouse-model phenotypes

Observed phenotypes of the mouse ortholog (MGI:1922579) from MGI (Alliance of Genome Resources) — knockout/mutant phenotypes, ranked by annotation count. 8 distinct phenotype terms.

Mouse phenotype (MP)	Records
small testis	1
small seminiferous tubules	1
abnormal spermatogenesis	1
male infertility	1
arrest of male meiosis	1
abnormal chromosomal synapsis	1
abnormal X-Y chromosome synapsis during male meiosis	1
decreased spermatid number	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
Gallus gallus	Q5ZIE8	75.2%	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
TEKT5	protein-coding	146279
EMP2	protein-coding	2013
GRIN2A	protein-coding	2903
LINC01290	ncRNA	106144584

Protein

Protein identifiers

Activating transcription factor 7-interacting protein 2 — Q5U623 (reviewed: Q5U623)

Alternative names: MBD1-containing chromatin-associated factor 2

All UniProt accessions (8): Q5U623, B4DKH3, F5GY73, H3BNE6, H3BPC9, H3BR07, H3BUP1, I3L4M8

UniProt curated annotations — full annotation on UniProt →

Function. Recruiter that couples transcriptional factors to general transcription apparatus and thereby modulates transcription regulation and chromatin formation. Can both act as an activator or a repressor depending on the context. Mediates MBD1-dependent transcriptional repression, probably by recruiting complexes containing SETDB1. The complex formed with MBD1 and SETDB1 represses transcription and probably couples DNA methylation and histone H3 ‘Lys-9’ trimethylation (H3K9me3) activity.

Subunit / interactions. Interacts with MBD1, SETDB1 and SP1. Probably forms a complex with SETDB1 and MBD1.

Subcellular location. Nucleus.

Similarity. Belongs to the MCAF family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q5U623-1	1	yes
Q5U623-2	2

RefSeq proteins (4): NP_001243089, NP_001339049, NP_001380648, NP_079273 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR003961	FN3_dom	Domain
IPR026085	ATF7-int	Family
IPR031870	ATF7IP_BD	Domain
IPR056565	Fn3_ATF7IP	Domain

Pfam: PF16788, PF16794

UniProt features (21 total): compositionally biased region 4, modified residue 3, sequence variant 3, sequence conflict 3, region of interest 3, splice variant 2, chain 1, domain 1, coiled-coil region 1

Structure

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5U623-F1	56.88	0.21

Human Protein Atlas

Protein class: Predicted intracellular proteins

Protein evidence: Evidence at protein level

Antibody reliability (HPA): IH enhanced

Functional residue map

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

Post-translational modifications (3)

Type	Positions
Phosphoserine	416, 488, 521

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: 141 (showing top): TGCTGCT_MIR15A_MIR16_MIR15B_MIR195_MIR424_MIR497, MARTINEZ_RB1_TARGETS_DN, ROZANOV_MMP14_TARGETS_UP, HELLER_HDAC_TARGETS_SILENCED_BY_METHYLATION_UP, GOCC_TRANSCRIPTION_REGULATOR_COMPLEX, DODD_NASOPHARYNGEAL_CARCINOMA_DN, KRIGE_RESPONSE_TO_TOSEDOSTAT_6HR_DN, WANG_RESPONSE_TO_GSK3_INHIBITOR_SB216763_UP, LEE_DIFFERENTIATING_T_LYMPHOCYTE, SMIRNOV_RESPONSE_TO_IR_2HR_DN, GOMF_TRANSCRIPTION_COREGULATOR_ACTIVITY, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, ASH1L_TARGET_GENES, CAVIN1_TARGET_GENES, CBX5_TARGET_GENES

GO Biological Process (2): DNA-templated transcription (GO:0006351), regulation of DNA-templated transcription (GO:0006355)

GO Molecular Function (2): transcription coregulator activity (GO:0003712), protein binding (GO:0005515)

GO Cellular Component (2): nucleus (GO:0005634), transcription regulator complex (GO:0005667)

GO top-level categories

9 GO namespaces:

Category	Terms
gene expression	1
RNA biosynthetic process	1
DNA-templated transcription	1
regulation of gene expression	1
regulation of RNA biosynthetic process	1
transcription regulator activity	1
binding	1
intracellular membrane-bounded organelle	1
protein-containing complex	1

Protein interactions and networks

STRING

showing 15 of 458 interactions by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ATF7IP2	SETDB1	Q15047	839
ATF7IP2	GTF2E2	P29084	639
ATF7IP2	GTF2E1	P29083	552
ATF7IP2	RASGEF1A	Q8N9B8	517
ATF7IP2	GLIPR1L2	Q4G1C9	493
ATF7IP2	DBNDD1	Q9H9R9	451
ATF7IP2	TCEAL1	Q15170	446
ATF7IP2	DEXI	O95424	446
ATF7IP2	ATF7	P17544	433
ATF7IP2	ERCC3	P19447	427
ATF7IP2	ERCC2	P18074	427
ATF7IP2	CBX1	P23197	427
ATF7IP2	SUMO2	P55855	382
ATF7IP2	PDXDC1	Q6P996	376
ATF7IP2	BBX	Q8WY36	371

IntAct

Human interaction partners of ATF7IP2 in IntAct, one row per partner (best MIscore; records = supporting IntAct interaction records).

6 partners by confidence:

Partner	Interaction type	MIscore	Records
MAP1LC3A	direct interaction	0.440	1
H2BC9	physical association	0.400	1
RCN1	physical association	0.400	1
SSR3	physical association	0.400	1
SETDB1	association	0.350	1
BIN1	physical association	0.000	1

BioGRID (23 interactions; top human partners by supporting records): SETDB1 (Affinity Capture-MS; 3 records), ARL14EP (Affinity Capture-MS; 2 records), MBD1 (Reconstituted Complex; 2 records), SP1 (Affinity Capture-Western; 2 records), AGO2 (Affinity Capture-RNA), ATF7IP (Affinity Capture-MS), DDX58 (Affinity Capture-RNA), EGFR (Affinity Capture-MS), EZR (Cross-Linking-MS (XL-MS)), FSD2 (Two-hybrid), MAP1LC3A (Protein-peptide), MED4 (Two-hybrid), NUDT21 (Affinity Capture-RNA), NUP62 (Two-hybrid), SETD3 (Affinity Capture-MS)

Protein complexes (CORUM) (1)

Experimentally-characterized complexes this protein is a subunit of (★ = the complex contains a known drug target).

1 complexes by size:

Complex	Subunits	Members
SP1-MCAF2 complex	2	ATF7IP2, SP1

Disease & clinical

Genetic variants

Variant evidence for ATF7IP2: 160 ClinVar records (1 pathogenic / likely pathogenic); 5 GWAS associations. Per-variant detail is on Sugi Variant.

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	123
Likely benign	18
Benign	0

Top pathogenic / likely-pathogenic (1)

Showing all 1 pathogenic / likely-pathogenic ClinVar records, ranked by ClinVar review status (expert panel → multiple submitters → single submitter), then by number of submitting labs.

Variant ID	HGVS	Classification	Review	Submitters
688399	GRCh37/hg19 16p13.13(chr16:10563055-10958954)x1	Pathogenic	no assertion criteria provided	1

Per-variant reference — Sugi Variant

Explore ATF7IP2’s pathogenic and likely-pathogenic variants individually — each with its ClinVar classification and conditions, applied ACMG criteria (ClinGen expert panel, where curated), the calibrated in-silico predictors (AlphaMissense, REVEL, SaProt, conservation), gnomAD frequency, and the predictor-disagreement QC signal — on Sugi Variant.

SpliceAI

Top 10 splice-impact sites by Δscore (adjacent positions with the same effect merged into one range; 34 predictions of 1,548):

Position(s)	Effect	Δscore	Sites
16:10438236–10438237	donor_loss	1.0000	5
16:10457478	donor_gain	1.0000
16:10473477–10473478	acceptor_loss	1.0000	3
16:10473535–10473536	donor_loss	1.0000	5
16:10473911–10473913	acceptor_gain	1.0000	2
16:10473922	acceptor_loss	1.0000
16:10473990–10473991	donor_loss	1.0000	5
16:10430609–10430610	acceptor_loss	0.9900	6
16:10431456–10431457	donor_loss	0.9900	5
16:10433512	acceptor_gain	0.9900

AlphaMissense

69 missense substitutions predicted likely pathogenic (of 548 scored), across 17 residues. Top 17 hotspot residues, ranked by the number of likely-pathogenic substitutions (of those reachable by a single-nucleotide change), then by mean score:

Residue	Likely-pathogenic substitutions	Mean am_pathogenicity	Max am_pathogenicity
K16	6	0.965	0.984
M18	6	0.951	0.976
T17	6	0.892	0.954
K13	6	0.877	0.969
K15	6	0.872	0.972
A14	6	0.846	0.982
Q25	5	0.723	0.834
R23	4	0.830	0.986
S21	4	0.792	0.866
P19	4	0.780	0.839
K10	4	0.684	0.755
S3	3	0.750	0.750
I11	3	0.629	0.694
C22	2	0.690	0.781
K24	2	0.653	0.653
L12	1	0.964	0.964
L29	1	0.867	0.867

HPA cancer prognostics

RNA cancer specificity: Low cancer specificity

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

1 prognostic cancer types:

Cancer	Prognostic	p-value
Rectum Adenocarcinoma (TCGA)	favorable	8.64e-05

Disease associations

OMIM: gene MIM:613645 | disease phenotypes:

GWAS associations

5 associations:

Study	Trait	p-value
GCST005358_2	Disease progression to choroidal neovascularization form in age-related macular degeneration	3e-8
GCST000618_27	Response to antipsychotic treatment	7e-7
GCST002938_6	Copper levels	7e-7
GCST009144_33	Disease progression in age-related macular degeneration (adjusted for baseline)	8e-7
GCST003542_10	Night sleep phenotypes	9e-6

EFO canonical traits (from GWAS)

1 canonical traits:

EFO ID	Trait name
EFO:0008336	disease progression measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (CPIC guideline: no)

CTD chemical–gene interactions

27 total (human), top 27 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, affects cotreatment, increases abundance	2
Cadmium Chloride	increases expression	2
pirinixic acid	affects binding, increases activity, increases expression	1
2-methyl-4-isothiazolin-3-one	increases expression	1
trichostatin A	increases expression	1
manganese chloride	increases abundance, affects cotreatment, decreases expression	1
potassium chromate(VI)	increases expression	1
ciglitazone	affects binding, increases expression	1
CGP 52608	affects binding, increases reaction	1
abrine	increases expression	1
(4-amino-1,4-dihydro-3-(2-pyridyl)-5-thioxo-1,2,4-triazole)copper(II)	increases expression	1
jinfukang	decreases expression	1
(+)-JQ1 compound	increases expression	1
Leflunomide	increases expression	1
Acetaminophen	increases expression	1
Arsenic	decreases expression, increases abundance, affects cotreatment	1
Benzo(a)pyrene	affects methylation	1
Doxorubicin	decreases expression	1
Manganese	affects cotreatment, decreases expression, increases abundance	1
Tobacco Smoke Pollution	decreases expression	1
Valproic Acid	increases expression	1
Vanadates	decreases expression	1
Cyclosporine	decreases expression	1
Okadaic Acid	increases expression	1
Copper Sulfate	affects expression	1
Acrylamide	increases expression	1
Particulate Matter	decreases expression	1

Clinical trials (associated diseases)

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