ATMIN

Summary

ATMIN (ATM interactor, HGNC:29034) is a protein-coding gene on chromosome 16q23.2, encoding ATM interactor (O43313). Transcription factor. It is a selective cancer dependency (DepMap: 15.5% of cell lines).

Enables dynein complex binding activity. Involved in positive regulation of DNA-templated transcription. Located in nuclear body.

Source: NCBI Gene 23300 — automated summary from GO annotations (Alliance of Genome Resources).

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 177 total — 1 likely-pathogenic
• GTEx eGene: eQTL in 28 tissues, sQTL in 3 (q < 0.05)
• Cancer dependency (DepMap): dependent in 15.5% of screened cell lines
• Constraint (gnomAD): pLI 0.00 (LoF-tolerant), LOEUF 0.69 (unconstrained)
• MANE Select transcript: NM_015251
• Notable: 177 clinical variants but no curated precision-oncology (CIViC) evidence yet

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29034
Approved symbol	ATMIN
Name	ATM interactor
Location	16q23.2
Locus type	gene with protein product
Status	Approved
Aliases	ASCIZ, KIAA0431, ZNF822
Ensembl gene	ENSG00000166454
Ensembl biotype	protein_coding
OMIM	614693
Entrez	23300

Gene structure

Transcript identifiers

Ensembl transcripts: 16 — 9 protein_coding, 5 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined, 1 retained_intron

MANE Select: ENST00000299575

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

ENST00000299575, ENST00000539819, ENST00000562969, ENST00000564241, ENST00000565237, ENST00000566488, ENST00000946484, ENST00001023853, ENST00001023854, ENST00001023855, ENST00001023856, ENST00001062234, ENST00001062235, ENST00001062236, ENST00001126572, ENST00001139964

RefSeq mRNA: 2 — MANE Select: NM_015251 NM_001300728, NM_015251

CCDS: CCDS32494, CCDS73917

Canonical transcript exons

ENST00000299575 — 4 exons

Exon	Start	End
ENSE00001298724	81035842	81036206
ENSE00002588712	81043161	81047350
ENSE00003584890	81042281	81042480
ENSE00003590968	81041356	81041481

Expression profiles

Bgee: expression breadth ubiquitous, 299 present calls, max score 97.32.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 14.3851 / max 178.4977, expressed in 1795 samples.

Highest expression (Bgee): sperm, male germ cell, Brodmann (1909) area 23, amniotic fluid, gingival epithelium.

Genetic regulation across tissues (GTEx eQTL / sQTL)

ATMIN is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 28 tissues and its splicing (sQTL) in 3 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

showing 20 of 31 significant tissue × QTL associations:

Tissue	QTL	q-value	Slope	Lead variant
Muscle Skeletal	eqtl	1.3e-98	-0.81	16:81046761:T:C
Thyroid	eqtl	1.1e-12	+0.27	16:81040555:T:G
Brain Nucleus accumbens basal ganglia	eqtl	6.5e-12	+0.54	16:81041195:A:G
Testis	sqtl	3.8e-11	-0.95	16:81039139:G:A
Heart Atrial Appendage	eqtl	2.9e-06	-0.21	16:81106827:T:TA
Small Intestine Terminal Ileum	eqtl	2.4e-05	+0.26	16:81024565:T:TCAACTCAGC
Brain Cortex	eqtl	3.0e-05	+0.34	16:81093976:G:A
Brain Hypothalamus	eqtl	7.2e-05	+0.27	16:81066108:T:C
Brain Caudate basal ganglia	eqtl	8.1e-05	+0.34	16:81041195:A:G
Pancreas	eqtl	9.2e-05	+0.22	16:81035143:T:C
Brain Putamen basal ganglia	eqtl	1.0e-04	+0.42	16:81093378:T:C
Esophagus Mucosa	eqtl	1.8e-04	-0.31	16:81052785:G:C
Testis	eqtl	3.7e-04	+0.14	16:81037092:A:G
Brain Frontal Cortex BA9	eqtl	1.3e-03	-0.37	16:81031454:A:G
Cells Cultured fibroblasts	eqtl	1.3e-03	+0.17	16:81034525:A:T
Brain Cerebellum	eqtl	2.4e-03	+0.24	16:80999471:C:T
Colon Transverse	eqtl	3.5e-03	-0.39	16:80959516:C:A
Cells EBV-transformed lymphocytes	eqtl	3.6e-03	+0.25	16:81074143:T:C
Nerve Tibial	eqtl	3.7e-03	+0.14	16:81103437:T:C
Whole Blood	eqtl	5.0e-03	+0.44	16:81031707:C:T

FANTOM5 promoters

2 alternative TSS:

Promoter ID	TPM avg	Samples expressed
155135	14.3750	1795
155136	0.0101	3

Top tissues by expression

showing 100 of 301 tissues by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	97.32	gold quality
male germ cell	CL:0000015	96.59	gold quality
Brodmann (1909) area 23	UBERON:0013554	96.34	gold quality
amniotic fluid	UBERON:0000173	95.88	gold quality
gingival epithelium	UBERON:0001949	94.54	gold quality
palpebral conjunctiva	UBERON:0001812	94.43	gold quality
germinal epithelium of ovary	UBERON:0001304	94.11	gold quality
cortical plate	UBERON:0005343	93.99	gold quality
eye	UBERON:0000970	93.89	gold quality
gingiva	UBERON:0001828	93.72	gold quality
substantia nigra pars compacta	UBERON:0001965	93.55	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	93.53	gold quality
pons	UBERON:0000988	93.52	gold quality
right testis	UBERON:0004534	92.91	gold quality
middle temporal gyrus	UBERON:0002771	92.71	gold quality
left testis	UBERON:0004533	92.66	gold quality
primary visual cortex	UBERON:0002436	92.65	gold quality
ganglionic eminence	UBERON:0004023	92.39	gold quality
testis	UBERON:0000473	92.31	gold quality
pigmented layer of retina	UBERON:0001782	92.29	gold quality
retina	UBERON:0000966	92.27	gold quality
islet of Langerhans	UBERON:0000006	92.23	gold quality
substantia nigra pars reticulata	UBERON:0001966	91.94	gold quality
occipital lobe	UBERON:0002021	91.82	gold quality
medial globus pallidus	UBERON:0002477	91.74	gold quality
esophagus squamous epithelium	UBERON:0006920	91.67	gold quality
placenta	UBERON:0001987	91.55	gold quality
superior vestibular nucleus	UBERON:0007227	91.41	gold quality
lateral nuclear group of thalamus	UBERON:0002736	91.34	gold quality
globus pallidus	UBERON:0001875	91.26	gold quality
CA1 field of hippocampus	UBERON:0003881	91.23	gold quality
endothelial cell	CL:0000115	90.88	gold quality
oral cavity	UBERON:0000167	90.66	gold quality
parietal pleura	UBERON:0002400	90.58	gold quality
prefrontal cortex	UBERON:0000451	90.56	gold quality
choroid plexus epithelium	UBERON:0003911	90.55	gold quality
secondary oocyte	CL:0000655	90.44	gold quality
lateral globus pallidus	UBERON:0002476	90.36	gold quality
epithelium of esophagus	UBERON:0001976	90.32	gold quality
upper leg skin	UBERON:0004262	90.20	gold quality
cerebellar vermis	UBERON:0004720	90.19	gold quality
rectum	UBERON:0001052	90.18	gold quality
skin of hip	UBERON:0001554	90.17	gold quality
endometrium epithelium	UBERON:0004811	90.17	gold quality
squamous epithelium	UBERON:0006914	90.09	gold quality
endometrium	UBERON:0001295	90.08	gold quality
penis	UBERON:0000989	89.83	gold quality
pleura	UBERON:0000977	89.79	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	89.74	gold quality
corpus callosum	UBERON:0002336	89.58	gold quality
epithelium of nasopharynx	UBERON:0001951	89.57	gold quality
nasopharynx	UBERON:0001728	89.56	gold quality
gastrocnemius	UBERON:0001388	89.55	gold quality
muscle of leg	UBERON:0001383	89.52	gold quality
corpus epididymis	UBERON:0004359	89.48	gold quality
subthalamic nucleus	UBERON:0001906	89.32	gold quality
Brodmann (1909) area 9	UBERON:0013540	89.30	gold quality
smooth muscle tissue	UBERON:0001135	89.27	gold quality
cerebral cortex	UBERON:0000956	89.26	gold quality
neocortex	UBERON:0001950	89.22	gold quality
superior frontal gyrus	UBERON:0002661	89.16	gold quality
medulla oblongata	UBERON:0001896	89.12	gold quality
hypothalamus	UBERON:0001898	89.11	gold quality
frontal cortex	UBERON:0001870	89.06	gold quality
frontal lobe	UBERON:0016525	89.06	gold quality
renal glomerulus	UBERON:0000074	89.05	gold quality
telencephalon	UBERON:0001893	88.91	gold quality
tibialis anterior	UBERON:0001385	88.89	gold quality
calcaneal tendon	UBERON:0003701	88.86	gold quality
midbrain	UBERON:0001891	88.82	gold quality
substantia nigra	UBERON:0002038	88.81	gold quality
jejunal mucosa	UBERON:0000399	88.79	gold quality
cingulate cortex	UBERON:0003027	88.78	gold quality
metanephric glomerulus	UBERON:0004736	88.78	gold quality
forebrain	UBERON:0001890	88.74	gold quality
inferior vagus X ganglion	UBERON:0005363	88.72	gold quality
lower lobe of lung	UBERON:0008949	88.71	gold quality
anterior cingulate cortex	UBERON:0009835	88.69	gold quality
mammary duct	UBERON:0001765	88.65	gold quality
amygdala	UBERON:0001876	88.63	gold quality
stromal cell of endometrium	CL:0002255	88.60	gold quality
Ammon’s horn	UBERON:0001954	88.60	gold quality
brain	UBERON:0000955	88.57	gold quality
pancreas	UBERON:0001264	88.53	gold quality
central nervous system	UBERON:0001017	88.50	gold quality
parietal lobe	UBERON:0001872	88.50	gold quality
visceral pleura	UBERON:0002401	88.49	gold quality
temporal lobe	UBERON:0001871	88.46	gold quality
esophagus mucosa	UBERON:0002469	88.44	gold quality
dorsal plus ventral thalamus	UBERON:0001897	88.35	gold quality
deltoid	UBERON:0001476	88.32	gold quality
epithelium of mammary gland	UBERON:0003244	88.31	gold quality
thoracic mammary gland	UBERON:0005200	88.28	gold quality
dorsal root ganglion	UBERON:0000044	88.24	gold quality
urinary bladder	UBERON:0001255	88.23	gold quality
right frontal lobe	UBERON:0002810	88.17	gold quality
superficial temporal artery	UBERON:0001614	88.15	gold quality
caudate nucleus	UBERON:0001873	88.15	gold quality
mammary gland	UBERON:0001911	88.14	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	88.12	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	9.19
E-MTAB-7303	no	319.81

HPA expression

RNA tissue specificity: Low tissue specificity

showing 60 of 79 HPA tissues / cells by nTPM:

Tissue / cell	Axis	nTPM	Protein (IHC)
Locus coeruleus	tissue	43.3
Postcentral gyrus	tissue	43.0
Frontal cortex	tissue	33.8
Hippocampus	tissue	33.7	low
Caudate putamen	tissue	30.0
Nucleus accumbens	tissue	29.4
Pons	tissue	26.0
Parathyroid gland	tissue	25.4	not detected
Choroid plexus	tissue	25.3
Hypothalamus	tissue	25.1
Cerebral cortex	tissue	25.0	medium
Somatosensory cortex	tissue	25.0
Occipital cortex	tissue	25.0
Prefrontal cortex	tissue	23.9
Motor cortex	tissue	23.8
Hippocampal formation	tissue	23.3
Entorhinal cortex	tissue	23.3
Thalamus	tissue	23.2
Superior colliculi	tissue	23.2
Temporal cortex	tissue	22.7
Retrosplenial and cingulate cortex	tissue	22.6
Midbrain	tissue	22.1
Substantia nigra	tissue	22.1
Septum	tissue	21.9
Periaqueductal gray	tissue	21.8
Retrosplenial cortex	tissue	21.8
Cerebellum	tissue	21.6	medium
Insular cortex	tissue	21.3
Testis	tissue	21.1	high
Ventral forebrain	tissue	20.5
Medulla oblongata	tissue	20.2
Amygdala	tissue	19.9
Basal ganglia	tissue	19.7	not detected
Thyroid gland	tissue	19.3	medium
Placenta	tissue	19.2	medium
Putamen	tissue	19.1
Kidney	tissue	18.4	medium
Esophagus	tissue	17.8	medium
Spinal cord	tissue	17.4
Epididymis	tissue	16.9	low
Liver	tissue	16.8	low
Skin 1	tissue	16.6	medium
Prostate	tissue	16.5	low
Olfactory bulb	tissue	16.4
Tongue	tissue	15.9
Pancreas	tissue	15.2	low
Adipose tissue	tissue	14.9	not detected
Skeletal muscle	tissue	14.9	medium
Corpus callosum	tissue	14.7
Thymus	tissue	14.6
Tonsil	tissue	14.1	medium
Seminal vesicle	tissue	13.9	not detected
Breast	tissue	13.5	not detected
Heart muscle	tissue	13.3	medium
Urinary bladder	tissue	13.3	medium
Lymph node	tissue	13.0	low
Endometrium 1	tissue	12.9	medium
Rectum	tissue	12.8	medium
Smooth muscle	tissue	12.8	medium
Cervix	tissue	12.7	medium

Brain sub-regions (HPA Brain Atlas): detected in 191; highest nTPM — Periaquaductal grey, anterior (41.3), Median raphe nucleus (40.6), Arcuate nucleus (40.1), Ventromedial nucleus (39.6), Paramedian reticular nucleus (37.7).

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

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

showing 30 of 114 miRNAs:

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-6867-5P	100.00	82.21	3464
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-4533	100.00	69.48	2758
HSA-MIR-200B-3P	100.00	73.31	2693
HSA-MIR-200C-3P	100.00	73.35	2685
HSA-MIR-429	100.00	73.44	2698
HSA-MIR-34A-5P	99.99	71.21	1784
HSA-MIR-449A	99.99	71.05	1776
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-181A-5P	99.99	72.96	2995
HSA-MIR-181B-5P	99.99	72.97	2996
HSA-MIR-181C-5P	99.99	72.95	2996
HSA-MIR-181D-5P	99.99	73.04	2997
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-548AN	99.97	70.91	2817
HSA-MIR-34C-5P	99.97	70.45	1577
HSA-MIR-449B-5P	99.97	70.26	1580
HSA-MIR-302C-5P	99.97	72.56	3642
HSA-MIR-1250-3P	99.96	70.04	4038
HSA-MIR-302E	99.96	70.74	2669
HSA-MIR-3910	99.95	71.13	2227
HSA-MIR-23A-3P	99.95	74.24	3163
HSA-MIR-23B-3P	99.95	74.24	3163
HSA-MIR-23C	99.95	73.92	3192
HSA-MIR-4753-3P	99.90	71.03	3786
HSA-MIR-374A-5P	99.90	71.34	2923
HSA-MIR-3686	99.90	70.53	2432
HSA-MIR-374B-5P	99.90	69.98	2734

Functional genomics

gnomAD constraint: pLI 0.004, LOEUF 0.695, missense Z -0.507 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD

Regional missense constraint (gnomAD RMC): no regional variation along ENST00000299575 — one region, missense o/e 1.03. DepMap (CRISPR cell-line fitness): dependent in 15.5% of screened cell lines.

Most-dependent cell lines (DepMap gene-effect, lower = stronger; ≤ −0.5 shown): KP-N-SI9s (-1.187), EW-22 (-1.178), UPMD1 (-1.082), NCC-ES1-C1 (-1.07), BC-1 (-1.069), NZOV9 (-1.033), DB (-1.028), RPE1-ss119 (-1.021), Mac-2A (-1.008), UACC-62_DAB_TRAM_R (-0.966), SW403 (-0.947), NB6 (-0.93), UM-UC-16 (-0.911), ES5 (-0.895), RCH-ACV (-0.892).

Literature-anchored findings (GeneRIF, showing 21)

• ASCIZ acts as a lesion-specific focus scaffold in a Rad51-dependent pathway that resolves cytotoxic repair intermediates, most likely single-stranded DNA gaps, resulting from MLH1-dependent processing of base lesions. (PMID:15933716)
• ATM/ATR-Substrate Chk2-Interacting Zn2+-finger protein (ASCIZ) required for repair of abasic sites after methylating and oxidative DNA damage but not double-strand breaks. Forms DNA damage-induced foci with RAD51 and ssDNA. ASCIZ foci depend on MLH1. (PMID:15933716)
• ATMIN defines a novel NBS1-independent pathway of ATM signalling. (PMID:17525732)
• These data suggest that ASCIZ may affect the choice between competing base repair pathways in a manner that reduces the amount of substrates available for Ig gene conversion. (PMID:18433721)
• ASCIZ (ATMIN) is structurally related to the yeast ATM/ATR substrate Mdt1 (Pin4/Ybl051c); both proteins contain SQ/TQ cluster domains and interact with N-terminal FHA domains of CHK2/Rad53 kinases. (PMID:18728389)
• Absence of Asciz (Atmin) leads to increased oxidative and methylating DNA base damage sensitivity in primary fibroblasts (PMID:20975950)
• Asciz (Atmin) deletion or knock-down does not affect ATM levels and activation in mouse, chicken, or human cells (PMID:20975950)
• these results imply a potential cellular interference between DYNLL1 and ATMIN functions. (PMID:21971545)
• The ASCIZ-DYNLL1 feedback loop represents a novel mechanism for auto-regulation of gene expression, where the gene product directly inhibits the transcriptional activator while bound at its own promoter. (PMID:22167198)
• ATMIN is required for cell cycle progression and chromosome segregation following replication stress.ATMIN is required for the ATM-mediated signaling and recruitment of 53BP1 to DNA damage sites upon replication stress. (PMID:25262557)
• WRNIP1 connects PCNA monoubiquitination with ATMIN/ATM to activate ATM signalling in response to replication stress and contribute to the maintenance of genomic stability. (PMID:26549024)
• Repression of ATMIN in hypoxia is mediated by both p53 and HIF-1alpha in an oxygen dependent manner. (PMID:26875667)
• Studies suggest that ATM INteractor (ATMIN) could be an important biomarker in disease prognosis and treatment that might lighten the burden of chronic kidney disease and also affect on its progression. (PMID:27913685)
• The study results improve our understanding of the ATMIN-KRas axis leading to HNSCC migration or invasion and metastasis and facilitates the identification of possible therapy targets of downstream genes for designing effective therapeutic strategies in personalized medicine (PMID:28012797)
• ASCIZ/ATMIN is dispensable for ATM activation, and contradict the previously reported dependence of ATM on ASCIZ/ATMIN. (PMID:28648892)
• This work indicates a novel role for non-canonical Wnt/planar cell polarity signalling in Autosomal Recessive Polycystic Kidney Disease and suggests ATMIN as a modulator of PKHD1. (PMID:30414501)
• PPARgamma promotes ATM signaling and is essential for UBR5 activity targeting ATM interactor (ATMIN). (PMID:30699358)
• ATMIN is located close to FRA16D and is commonly lost in lung adenocarcinoma (LUAD)and was associated with reduced patient survival. ATMIN is a tumor suppressor in LUAD; fragility at chr16q23 correlates with loss of ATMIN in human LUAD. (PMID:31481498)
• ATMIN Suppresses Metastasis by Altering the WNT-Signaling Pathway via PARP1 in MSI-High Colorectal Cancer. (PMID:34148137)
• MicroRNA-361-5p slows down gliomas development through regulating UBR5 to elevate ATMIN protein expression. (PMID:34321465)
• Transcription factor ATMIN facilitates chemoresistance in nasopharyngeal carcinoma. (PMID:38321024)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	atmin	ENSDARG00000068601
mus_musculus	Atmin	ENSMUSG00000047388
rattus_norvegicus	Atmin	ENSRNOG00000011422

Paralogs (3): RIOK2 (ENSG00000058729), RIOK3 (ENSG00000101782), RIOK1 (ENSG00000124784)

Mouse-model phenotypes

Observed phenotypes of the mouse ortholog (MGI:2682328) from MGI (Alliance of Genome Resources) — knockout/mutant phenotypes, ranked by annotation count. 59 distinct phenotype terms.

Mouse phenotype (MP)	Records
exencephaly	4
absent lungs	3
abnormal craniofacial morphology	2
edema	2
left pulmonary isomerism	2
interrupted aortic arch	2
decreased B cell number	2
early cellular replicative senescence	2
decreased immature B cell number	2
lethality throughout fetal growth and development, complete penetrance	2
decreased cell proliferation	1
right pulmonary isomerism	1
small spleen	1
decreased body weight	1
microphthalmia	1
increased anxiety-related response	1
hyperactivity	1
thymus hypoplasia	1
premature death	1
abnormal eye morphology	1
abnormal B cell differentiation	1
neurodegeneration	1
abnormal B cell physiology	1
micrognathia	1
situs inversus	1

+34 more (showing top 25).

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
Arabidopsis thaliana	Q8RWX7	92.6%	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
CENPN-AS1	ncRNA	107984858
PKD1L2	protein-coding	114780
C16orf46	protein-coding	123775
GCSH	protein-coding	2653
CENPN	protein-coding	55839
ARLNC1	ncRNA	100996425
C16orf46-AS1	ncRNA	105371361
CMC2	protein-coding	56942
CDYL2	protein-coding	124359
BCO1	protein-coding	53630

Protein

Protein identifiers

ATM interactor — O43313 (reviewed: O43313)

Alternative names: ATM/ATR-substrate CHK2-interacting zinc finger protein, Zinc finger protein 822

All UniProt accessions (2): O43313, J3QRX7

UniProt curated annotations — full annotation on UniProt →

Function. Transcription factor. Plays a crucial role in cell survival and RAD51 foci formation in response to methylating DNA damage. Involved in regulating the activity of ATM in the absence of DNA damage. May play a role in stabilizing ATM. Binds to the DYNLL1 promoter and activates its transcription.

Subunit / interactions. Interacts via its C-terminus with ATM. Interacts with DYNLL1; this interaction inhibits ATMIN transcriptional activity and hence may play a role in a feedback loop whereby DYNLL1 inhibits transactivation of its own promoter by ATMIN.

Subcellular location. Nucleus.

Tissue specificity. Ubiquitously expressed in normal tissues and cancer cell lines with highest levels in placenta and skeletal muscle.

Isoforms (2)

UniProt ID	Names	Canonical?
O43313-1	1	yes
O43313-2	2

RefSeq proteins (2): NP_001287657, NP_056066* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR013087	Zf-C2H2_type	Domain
IPR055303	ATMIN	Family
IPR056380	Znf_C2H2_ASCIZ_4th	Domain
IPR056381	Znf_C2HC_ASCIZ_3rd	Domain
IPR056545	C2H2_ASCIZ_1st_2nd	Domain

Pfam: PF24757, PF24759, PF24761

UniProt features (23 total): sequence conflict 8, region of interest 5, compositionally biased region 4, zinc finger region 2, sequence variant 2, chain 1, splice variant 1

Structure

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-O43313-F1	47.67	0.01

Human Protein Atlas

Protein class: Predicted intracellular proteins

Protein evidence: Evidence at protein level

Subcellular location (HPA, imaging): nuclear bodies

Antibody reliability (HPA): IH approved · IF supported

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): GSE18804_SPLEEN_MACROPHAGE_VS_BRAIN_TUMORAL_MACROPHAGE_DN, GSE18804_SPLEEN_MACROPHAGE_VS_TUMORAL_MACROPHAGE_DN, GCM_MAP4K4, TATTATA_MIR374, GOBP_POSITIVE_REGULATION_OF_ORGANELLE_ORGANIZATION, GOBP_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, GOBP_POSITIVE_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, GOBP_REGULATION_OF_CELL_PROJECTION_ORGANIZATION, ONKEN_UVEAL_MELANOMA_UP, GOBP_CILIUM_ORGANIZATION, GOBP_DNA_DAMAGE_RESPONSE, GOBP_ORGANELLE_ASSEMBLY, GOBP_REGULATION_OF_CILIUM_ASSEMBLY, GOBP_MOTILE_CILIUM_ASSEMBLY, GOBP_CELL_PROJECTION_ORGANIZATION

GO Biological Process (5): DNA-templated transcription (GO:0006351), regulation of transcription by RNA polymerase II (GO:0006357), DNA damage response (GO:0006974), positive regulation of DNA-templated transcription (GO:0045893), positive regulation of transcription by RNA polymerase II (GO:0045944)

GO Molecular Function (7): transcription cis-regulatory region binding (GO:0000976), DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), DNA-binding transcription activator activity, RNA polymerase II-specific (GO:0001228), zinc ion binding (GO:0008270), dynein complex binding (GO:0070840), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (2): nucleus (GO:0005634), nuclear body (GO:0016604)

GO top-level categories

24 GO namespaces:

Category	Terms
regulation of DNA-templated transcription	2
transcription by RNA polymerase II	2
regulation of transcription by RNA polymerase II	2
RNA polymerase II transcription regulatory region sequence-specific DNA binding	2
gene expression	1
RNA biosynthetic process	1
cellular response to stress	1
DNA-templated transcription	1
positive regulation of RNA biosynthetic process	1
positive regulation of DNA-templated transcription	1
transcription regulatory region nucleic acid binding	1
sequence-specific double-stranded DNA binding	1
chromatin	1
DNA-binding transcription factor activity	1
DNA-binding transcription factor activity, RNA polymerase II-specific	1
DNA-binding transcription activator activity	1
positive regulation of transcription by RNA polymerase II	1
transition metal ion binding	1
protein-containing complex binding	1
binding	1
cation binding	1
intracellular membrane-bounded organelle	1
nucleoplasm	1
intracellular membraneless organelle	1

Experimentally-supported GO annotations

GO terms backed by direct experimental evidence (ECO experimental codes) — 3 of 14 annotations. The rest are phylogenetic / computational / electronic (IEA).

3 experimentally-supported GO terms:

GO term	NS	Evidence
positive regulation of DNA-templated transcription	BP	direct assay
nuclear body	CC	direct assay
dynein complex binding	MF	physical interaction

Protein interactions and networks

STRING

showing 15 of 492 interactions by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ATMIN	DYNLL1	P63167	604
ATMIN	WRNIP1	Q96S55	568
ATMIN	ATM	Q13315	558
ATMIN	UBR5	O95071	533
ATMIN	CHEK2	O96017	476
ATMIN	RAD18	Q9NS91	418
ATMIN	RAD50	Q92878	400
ATMIN	TP53BP1	Q12888	390
ATMIN	FAN1	Q9Y2M0	390
ATMIN	MDC1	Q14676	343
ATMIN	TP53RK	Q96S44	328
ATMIN	PRKDC	P78527	327
ATMIN	RNF168	Q8IYW5	321
ATMIN	FIBCD1	Q8N539	316
ATMIN	ATRIP	Q8WXE1	316

IntAct

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

3 partners by confidence:

Partner	Interaction type	MIscore	Records
ATM	physical association	0.560	5
BRAP	physical association	0.370	1
OAS2	association	0.350	1

BioGRID (25 interactions; top human partners by supporting records): UBR5 (Affinity Capture-Western; 4 records), ATM (Affinity Capture-Western; 2 records), CAPN13 (Affinity Capture-MS; 2 records), DYNLL1 (Affinity Capture-MS; 2 records), DYNLL2 (Affinity Capture-MS; 2 records), SPECC1L (Affinity Capture-MS; 2 records), WRNIP1 (Affinity Capture-Western; 2 records), AGO2 (Affinity Capture-RNA), BRAP (Two-hybrid), HNRNPL (Affinity Capture-RNA), LDLR (Positive Genetic), OAS2 (Affinity Capture-MS), OTUD5 (Affinity Capture-Western), PPARG (Affinity Capture-Western), TOP3B (Affinity Capture-RNA)

Disease & clinical

Genetic variants

Variant evidence for ATMIN: 177 ClinVar records (1 pathogenic / likely pathogenic); 5 GWAS associations. Per-variant detail is on Sugi Variant.

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	1
Uncertain significance	154
Likely benign	10
Benign	1

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
815850	GRCh37/hg19 16q23.2-23.3(chr16:80476611-82397606)x1	Likely pathogenic	no assertion criteria provided	1

Per-variant reference — Sugi Variant

Explore ATMIN’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; 28 predictions of 293):

Position(s)	Effect	Δscore	Sites
16:81036207	donor_loss	1.0000	2
16:81041354–81041355	acceptor_loss	1.0000	5
16:81036207–81036208	donor_loss	0.9900	3
16:81041355	acceptor_loss	0.9900
16:81041482–81041483	donor_loss	0.9900	6
16:81041481	donor_loss	0.9800	2
16:81042523	donor_gain	0.9800
16:81043159–81043160	acceptor_loss	0.9800	6
16:81042489	donor_gain	0.9600
16:81043152	acceptor_loss	0.9500

AlphaMissense

1,393 missense substitutions predicted likely pathogenic (of 5,413 scored), across 316 residues. Top 20 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
M103	9	0.960	0.999
H104	8	0.998	1.000
H155	8	0.998	1.000
H160	8	0.997	0.999
H109	8	0.996	0.999
H183	8	0.996	0.999
H208	8	0.995	0.999
F146	8	0.988	0.999
H214	8	0.988	0.995
D179	8	0.984	0.996
D701	8	0.952	0.985
N97	8	0.942	0.998
F149	8	0.939	0.998
D791	8	0.920	0.971
H220	8	0.906	0.985
F636	8	0.903	0.986
D669	8	0.898	0.955
F792	8	0.898	0.985
F700	8	0.896	0.978
D707	8	0.894	0.953

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
Kidney Renal Clear Cell Carcinoma (TCGA)	favorable	1.12e-05

Disease associations

OMIM: gene MIM:614693 | disease phenotypes:

GWAS associations

5 associations:

Study	Trait	p-value
GCST90002392_16	Mean corpuscular volume	7e-15
GCST90002390_270	Mean corpuscular hemoglobin	1e-11
GCST004602_186	Mean corpuscular volume	1e-10
GCST005962_55	Waist-to-hip ratio adjusted for BMI x sex x age interaction (4df test)	1e-6
GCST005958_4	Waist-to-hip ratio adjusted for BMI (age >50)	4e-6

EFO canonical traits (from GWAS)

4 canonical traits:

EFO ID	Trait name
EFO:0007788	BMI-adjusted waist-hip ratio
EFO:0008007	age at assessment
EFO:0008343	sex interaction measurement
EFO:0004527	mean corpuscular hemoglobin

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (CPIC guideline: no)

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	decreases methylation, increases expression, affects expression	3
dicrotophos	decreases expression	1
triphenyl phosphate	affects expression	1
sodium arsenite	increases expression	1
cobaltous chloride	increases expression	1
di-n-butylphosphoric acid	affects expression	1
deguelin	decreases expression	1
fenpyroximate	decreases expression	1
4-chloro-N-((4-(1,1-dimethylethyl)phenyl)methyl)-3-ethyl-1-methyl-1H-pyrazole-5-carboxamide	decreases expression	1
pyrimidifen	decreases expression	1
Sunitinib	increases expression	1
Leflunomide	decreases expression	1
Acetaminophen	increases expression	1
Air Pollutants	affects expression, increases abundance	1
Antimycin A	decreases expression	1
Benzo(a)pyrene	increases expression	1
Cadmium	decreases expression	1
Doxorubicin	decreases expression	1
Methyl Methanesulfonate	decreases expression	1
Ozone	affects expression, increases abundance	1
Rotenone	decreases expression	1
Selenium	affects cotreatment, increases expression, decreases expression	1
Dihydrotestosterone	increases expression	1
Tobacco Smoke Pollution	increases expression	1
Tretinoin	decreases expression	1
Vitamin E	decreases expression, affects cotreatment, increases expression	1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	increases expression	1
Cyclosporine	decreases expression	1
Cadmium Chloride	decreases expression	1
Lactic Acid	decreases expression	1

Clinical trials (associated diseases)

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