ABITRAM

Summary

ABITRAM (actin binding transcription modulator, HGNC:1364) is a protein-coding gene on chromosome 9q31.3, encoding Protein Abitram (Q9NX38). Actin-binding protein that regulates actin polymerization, filopodia dynamics and increases the branching of proximal dendrites of developing neurons.

Predicted to enable actin filament binding activity and actin monomer binding activity. Predicted to be involved in dendrite morphogenesis; regulation of actin filament polymerization; and regulation of filopodium assembly. Predicted to be located in growth cone. Predicted to be active in several cellular components, including dendrite; filopodium tip; and lamellipodium.

Source: NCBI Gene 54942 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 56 total
• MANE Select transcript: NM_017832

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:1364
Approved symbol	ABITRAM
Name	actin binding transcription modulator
Location	9q31.3
Locus type	gene with protein product
Status	Approved
Aliases	CG-8, FLJ20457, Simiate
Ensembl gene	ENSG00000119328
Ensembl biotype	protein_coding
OMIM	620392
Entrez	54942

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 7 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000322940, ENST00000374624, ENST00000445175, ENST00000466200, ENST00000899979, ENST00000919245, ENST00000964591, ENST00000964592

RefSeq mRNA: 2 — MANE Select: NM_017832 NM_001410990, NM_017832

CCDS: CCDS6774, CCDS94453

Canonical transcript exons

ENST00000322940 — 6 exons

Exon	Start	End
ENSE00000805974	108935638	108935689
ENSE00000805975	108936308	108936437
ENSE00000805976	108939196	108939272
ENSE00000805977	108939385	108939454
ENSE00001860780	108939549	108940954
ENSE00002078636	108934400	108934565

Expression profiles

Bgee: expression breadth ubiquitous, 287 present calls, max score 96.22.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 9.5280 / max 117.1167, expressed in 1770 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
97930	9.5280	1770

Top tissues by expression

288 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
bronchial epithelial cell	CL:0002328	96.22	gold quality
tongue squamous epithelium	UBERON:0006919	95.87	gold quality
epithelium of bronchus	UBERON:0002031	95.82	gold quality
bronchus	UBERON:0002185	95.48	gold quality
hair follicle	UBERON:0002073	94.55	gold quality
mucosa of paranasal sinus	UBERON:0005030	93.79	gold quality
secondary oocyte	CL:0000655	92.90	gold quality
nasal cavity epithelium	UBERON:0005384	92.88	gold quality
corpus epididymis	UBERON:0004359	92.79	gold quality
caput epididymis	UBERON:0004358	92.56	gold quality
gingival epithelium	UBERON:0001949	92.40	gold quality
parotid gland	UBERON:0001831	91.86	gold quality
squamous epithelium	UBERON:0006914	91.83	gold quality
sperm	CL:0000019	91.80	gold quality
gingiva	UBERON:0001828	91.73	gold quality
epithelium of nasopharynx	UBERON:0001951	91.61	gold quality
male germ cell	CL:0000015	91.56	gold quality
esophagus squamous epithelium	UBERON:0006920	91.38	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	91.32	gold quality
nasal cavity mucosa	UBERON:0001826	91.23	gold quality
heart right ventricle	UBERON:0002080	91.15	gold quality
epithelium of esophagus	UBERON:0001976	90.90	gold quality
right uterine tube	UBERON:0001302	90.73	gold quality
lateral nuclear group of thalamus	UBERON:0002736	90.71	gold quality
oocyte	CL:0000023	90.70	gold quality
germinal epithelium of ovary	UBERON:0001304	90.38	gold quality
cervix squamous epithelium	UBERON:0006922	90.33	gold quality
left lobe of thyroid gland	UBERON:0001120	90.30	gold quality
colonic mucosa	UBERON:0000317	90.28	gold quality
mucosa of sigmoid colon	UBERON:0004993	90.20	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	7.98

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

59 targeting ABITRAM, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-8068	99.98	73.85	2376
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-548N	99.98	71.94	4170
HSA-MIR-146A-5P	99.96	68.93	988
HSA-MIR-146B-5P	99.96	69.13	977
HSA-MIR-128-3P	99.95	71.17	2484
HSA-MIR-216A-3P	99.95	71.19	2505
HSA-MIR-7153-5P	99.94	68.89	1006
HSA-MIR-4778-3P	99.93	70.40	1818
HSA-MIR-3682-5P	99.93	67.97	1163
HSA-MIR-3686	99.90	70.53	2432
HSA-MIR-4493	99.90	66.48	977
HSA-MIR-3681-3P	99.88	70.46	2254
HSA-MIR-4699-3P	99.71	70.15	3142
HSA-MIR-567	99.63	68.57	1219
HSA-MIR-1827	99.63	68.57	3265
HSA-MIR-4687-3P	99.48	66.41	968
HSA-MIR-3182	99.40	68.15	2454
HSA-MIR-302A-5P	99.39	68.21	1913
HSA-MIR-2115-3P	99.31	69.68	2026
HSA-MIR-5582-5P	99.27	71.42	1879
HSA-MIR-329-5P	99.27	68.11	1597
HSA-MIR-6739-3P	99.22	68.84	1843
HSA-MIR-548L	99.06	70.90	2560
HSA-MIR-129-1-3P	98.86	68.41	779
HSA-MIR-129-2-3P	98.86	68.41	779
HSA-MIR-6715B-3P	98.80	68.07	1204
HSA-MIR-4742-3P	98.73	69.82	1803

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	abitram	ENSDARG00000070407
mus_musculus	Abitram	ENSMUSG00000038827
rattus_norvegicus	Abitram	ENSRNOG00000010532
drosophila_melanogaster	CG9288	FBGN0260464
caenorhabditis_elegans		WBGENE00018835

Protein

Protein identifiers

Protein Abitram — Q9NX38 (reviewed: Q9NX38)

Alternative names: Actin-binding transcription modulator, Protein Simiate

All UniProt accessions (3): Q9NX38, X6R8U7, X6REY2

UniProt curated annotations — full annotation on UniProt →

Function. Actin-binding protein that regulates actin polymerization, filopodia dynamics and increases the branching of proximal dendrites of developing neurons.

Subunit / interactions. Interacts with F-actin. Interacts with G-actin.

Subcellular location. Nucleus speckle. Cell projection. Lamellipodium. Nucleus. Growth cone. Dendrite.

Miscellaneous. Depletion of ABITRAM by siRNA or neutralizing antibodies results in cell death within a few hours.

Similarity. Belongs to the ABITRAM family.

RefSeq proteins (2): NP_001397919, NP_060302* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR011053	Single_hybrid_motif	Homologous_superfamily
IPR033753	GCV_H/Fam206	Family
IPR039169	Abitram	Family

Pfam: PF01597

UniProt features (1 total): chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9NX38-F1	80.21	0.10

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 122 (showing top): GOBP_DENDRITE_DEVELOPMENT, GOBP_REGULATION_OF_PROTEIN_POLYMERIZATION, GOBP_NEUROGENESIS, GOBP_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, MONNIER_POSTRADIATION_TUMOR_ESCAPE_UP, GOBP_REGULATION_OF_ACTIN_FILAMENT_BASED_PROCESS, GOBP_REGULATION_OF_ANATOMICAL_STRUCTURE_SIZE, GOBP_REGULATION_OF_CELL_PROJECTION_ORGANIZATION, GOBP_DENDRITE_MORPHOGENESIS, GOBP_ACTIN_FILAMENT_ORGANIZATION, GOBP_REGULATION_OF_PROTEIN_CONTAINING_COMPLEX_ASSEMBLY, GOMF_ACTIN_BINDING, GOCC_NEURON_PROJECTION, GOBP_CELL_PROJECTION_ORGANIZATION, GOBP_REGULATION_OF_CELL_PROJECTION_ASSEMBLY

GO Biological Process (3): regulation of actin filament polymerization (GO:0030833), dendrite morphogenesis (GO:0048813), regulation of filopodium assembly (GO:0051489)

GO Molecular Function (4): actin monomer binding (GO:0003785), actin filament binding (GO:0051015), actin binding (GO:0003779), protein binding (GO:0005515)

GO Cellular Component (7): nucleus (GO:0005634), nuclear speck (GO:0016607), lamellipodium (GO:0030027), dendrite (GO:0030425), growth cone (GO:0030426), filopodium tip (GO:0032433), cell projection (GO:0042995)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
actin binding	2
cellular anatomical structure	2
regulation of actin polymerization or depolymerization	1
actin filament polymerization	1
regulation of protein polymerization	1
dendrite development	1
cell morphogenesis involved in neuron differentiation	1
neuron projection morphogenesis	1
filopodium assembly	1
regulation of plasma membrane bounded cell projection assembly	1
protein-containing complex binding	1
cytoskeletal protein binding	1
binding	1
intracellular membrane-bounded organelle	1
nuclear ribonucleoprotein granule	1
cell leading edge	1
plasma membrane bounded cell projection	1
neuron projection	1
dendritic tree	1
site of polarized growth	1
distal axon	1
filopodium	1

Protein interactions and networks

STRING

549 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ABITRAM	FRRS1L	Q9P0K9	882
ABITRAM	PEX26	Q7Z412	879
ABITRAM	PEX6	Q13608	864
ABITRAM	SYNJ2BP	P57105	826
ABITRAM	SPRYD7	Q5W111	459
ABITRAM	CTNNAL1	Q9UBT7	453
ABITRAM	C8A	P07357	445
ABITRAM	HSDL1	Q3SXM5	443
ABITRAM	NIPAL3	Q6P499	406
ABITRAM	C8B	P07358	398
ABITRAM	NHERF4	Q86UT5	396
ABITRAM	ARMC1	Q9NVT9	393
ABITRAM	ZACN	Q401N2	386
ABITRAM	LGALS8	O00214	386
ABITRAM	ELP1	O95163	386

IntAct

23 interactions, top by confidence:

A	B	Type	Score
PUS10	ABITRAM	psi-mi:“MI:0915”(physical association)	0.740
HMBOX1	ABITRAM	psi-mi:“MI:0915”(physical association)	0.720
ABITRAM	HMBOX1	psi-mi:“MI:0915”(physical association)	0.720
PGCKA1	ABITRAM	psi-mi:“MI:0915”(physical association)	0.560
MESD	ABITRAM	psi-mi:“MI:0915”(physical association)	0.560
ABITRAM	POTEF	psi-mi:“MI:0914”(association)	0.530
	ABITRAM	psi-mi:“MI:0915”(physical association)	0.370
ABITRAM	FYN	psi-mi:“MI:0914”(association)	0.350
ABITRAM	HMBOX1	psi-mi:“MI:0915”(physical association)	0.000
ABITRAM	PGCKA1	psi-mi:“MI:0915”(physical association)	0.000
ABITRAM	PUS10	psi-mi:“MI:0915”(physical association)	0.000
PUS10	ABITRAM	psi-mi:“MI:0915”(physical association)	0.000
ABITRAM	MESD	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (26): HMBOX1 (Two-hybrid), FAM206A (Co-fractionation), PUS10 (Affinity Capture-MS), ZHX2 (Affinity Capture-MS), TAOK1 (Affinity Capture-MS), TAOK2 (Affinity Capture-MS), POTEF (Affinity Capture-MS), CBY1 (Affinity Capture-MS), FAM206A (Synthetic Lethality), FAM206A (Affinity Capture-MS), FAM206A (Two-hybrid), HMBOX1 (Two-hybrid), C4orf19 (Two-hybrid), PUS10 (Two-hybrid), PUS10 (Affinity Capture-MS)

ESM2 similar proteins: A0A8I5ZNK2, A1YFX9, A6QLH6, B0BNF8, D3ZAW2, O43502, O88600, P08760, P11183, P20821, P23434, P27465, P33124, P34932, P97679, Q28DS0, Q28G67, Q29S16, Q2KIK0, Q2TFN9, Q571F8, Q5I0K3, Q5I0P2, Q5NVK4, Q5R8I8, Q5RDM4, Q5RFI8, Q5RFS0, Q5ZHW7, Q61316, Q6GR35, Q80ZQ9, Q86WA6, Q8BSF4, Q8JGT5, Q8K1Z0, Q8N0X4, Q8R2J9, Q8R4N0, Q91WC3

Diamond homologs: P34452, Q54TD9, Q5RFS0, Q9NX38, Q9VFR1, B1GYV6, B5Y8S2, Q1LU93, Q28G67, Q29S16, Q5ZHW7, Q6GR35, Q80ZQ9, Q9YDG2, A2BTQ0, A2BZ55, A3PFF7, A8G7H4, A9B2Q6, Q317X3, B2I6Q0, Q87EZ7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	43
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1277 predictions. Top by Δscore:

Variant	Effect	Δscore
9:108934561:ACCGG:A	donor_gain	1.0000
9:108934562:CCGG:C	donor_gain	1.0000
9:108934563:CGG:C	donor_gain	1.0000
9:108934564:GG:G	donor_gain	1.0000
9:108934564:GGG:G	donor_gain	1.0000
9:108934565:GG:G	donor_gain	1.0000
9:108934565:GGT:G	donor_loss	1.0000
9:108934566:G:GG	donor_gain	1.0000
9:108934566:G:T	donor_loss	1.0000
9:108934567:T:A	donor_loss	1.0000
9:108936434:GCGG:G	donor_gain	1.0000
9:108939192:ACAG:A	acceptor_gain	1.0000
9:108939192:ACAGG:A	acceptor_gain	1.0000
9:108939193:C:G	acceptor_gain	1.0000
9:108939194:AGG:A	acceptor_gain	1.0000
9:108939194:AGGG:A	acceptor_gain	1.0000
9:108939195:GGG:G	acceptor_gain	1.0000
9:108939195:GGGG:G	acceptor_gain	1.0000
9:108939383:A:AG	acceptor_gain	1.0000
9:108939384:G:GG	acceptor_gain	1.0000
9:108939384:GTT:G	acceptor_gain	1.0000
9:108939384:GTTGT:G	acceptor_gain	1.0000
9:108939545:CCA:C	acceptor_loss	1.0000
9:108939546:CA:C	acceptor_loss	1.0000
9:108939547:A:AG	acceptor_gain	1.0000
9:108939548:G:A	acceptor_loss	1.0000
9:108939548:G:GA	acceptor_gain	1.0000
9:108939548:GC:G	acceptor_gain	1.0000
9:108939548:GCC:G	acceptor_gain	1.0000
9:108939548:GCCAT:G	acceptor_gain	1.0000

AlphaMissense

1180 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
9:108936424:G:A	G83E	1.000
9:108936434:G:C	K86N	1.000
9:108936434:G:T	K86N	1.000
9:108939571:C:A	A144E	1.000
9:108935679:C:G	H41D	0.999
9:108935680:A:G	H41R	0.999
9:108935681:C:A	H41Q	0.999
9:108935681:C:G	H41Q	0.999
9:108935687:C:A	N43K	0.999
9:108935687:C:G	N43K	0.999
9:108935689:G:C	R44P	0.999
9:108936316:T:A	V47D	0.999
9:108936403:G:C	R76T	0.999
9:108936404:A:C	R76S	0.999
9:108936404:A:T	R76S	0.999
9:108936424:G:T	G83V	0.999
9:108936426:A:G	K84E	0.999
9:108936432:A:G	K86E	0.999
9:108936436:G:C	R87P	0.999
9:108939200:C:A	A89E	0.999
9:108939209:T:C	L92P	0.999
9:108939227:T:A	L98H	0.999
9:108939271:A:C	S113R	0.999
9:108939385:T:A	S113R	0.999
9:108939385:T:G	S113R	0.999
9:108939390:T:A	V115D	0.999
9:108939395:G:A	G117R	0.999
9:108939395:G:C	G117R	0.999
9:108939396:G:A	G117E	0.999
9:108939402:T:C	L119S	0.999

dbSNP variants (sampled 300 via entrez): RS1000011525 (9:108938622 G>A), RS1000031681 (9:108935848 T>G), RS1000154177 (9:108946347 T>A), RS1000180429 (9:108936173 G>A), RS1000204190 (9:108944264 A>G), RS1000258177 (9:108946008 A>C,G,T), RS1000683729 (9:108932898 C>T), RS1001156497 (9:108944583 GGAGAAGTA>G), RS1001172688 (9:108946115 A>T), RS1001478715 (9:108937116 C>T), RS1001628063 (9:108940118 G>A), RS1001803593 (9:108936720 G>A), RS1002914543 (9:108936836 A>G), RS1002957811 (9:108947882 C>T), RS1003188282 (9:108949259 C>T)

Disease associations

OMIM: gene MIM:620392 | disease phenotypes: MIM:616981

GenCC curated gene-disease

Mondo (2): developmental and epileptic encephalopathy, 37 (MONDO:0014859), optic atrophy (MONDO:0003608)

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D009896	Optic Atrophy	C10.292.700.225; C11.640.451

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

17 total (human), top 17 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
GSK-J4	increases expression	1
potassium chromate(VI)	increases expression	1
perfluorooctane sulfonic acid	increases expression	1
perfluoro-n-nonanoic acid	increases expression	1
ICG 001	increases expression	1
Sunitinib	increases expression	1
Air Pollutants	decreases expression, increases abundance	1
Doxorubicin	decreases expression	1
Ethyl Methanesulfonate	increases expression	1
Formaldehyde	increases expression	1
Methyl Methanesulfonate	increases expression	1
Tunicamycin	increases expression	1
Valproic Acid	decreases methylation	1
Vanadates	decreases expression	1
Cyclosporine	increases expression	1
Aflatoxin B1	increases methylation	1
Particulate Matter	decreases expression, increases abundance	1

Clinical trials (associated diseases)

10 trials via MONDO — disease-level, not drug-specific.

Trial	Phase	Status	Title
NCT01064505	PHASE1	COMPLETED	Safety Study of a Single IVT Injection of QPI-1007 in Chronic Optic Nerve Atrophy and Recent Onset NAION Patients
NCT05147701	PHASE1	RECRUITING	Safety of Cultured Allogeneic Adult Umbilical Cord Derived Mesenchymal Stem Cells for NAION
NCT02882477	PHASE2/PHASE3	UNKNOWN	Treatment of Wolfram Syndrome Type 2 With the Chelator Deferiprone and Incretin Based Therapy
NCT01834079	PHASE1/PHASE2	UNKNOWN	Study the Safety and Efficacy of Bone Marrow Derived Autologous Cells for the Treatment of Optic Nerve Disease
NCT04680143	PHASE1/PHASE2	COMPLETED	Systemic Erythropoietin Injection in Patients Having Optic Atrophy
NCT03011541	Not specified	RECRUITING	Stem Cell Ophthalmology Treatment Study II
NCT04580979	Not specified	COMPLETED	Natural History Study of FDXR Mutation-related Mitochondriopathy
NCT04594590	Not specified	COMPLETED	Natural History Study of SLC25A46 Mutation-related Mitochondriopathy
NCT04723160	Not specified	COMPLETED	Computer Aided Diagnosis of Multiple Eye Fundus Diseases From Color Fundus Photograph
NCT06390579	Not specified	COMPLETED	Building Research With Artificial Intelligence in Neuro-Ophthalmology