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 — automated summary from GO annotations (Alliance of Genome Resources).

At a glance

• Clinical variants (ClinVar): 59 total — 1 likely-pathogenic
• GTEx eGene: eQTL in 27 tissues, sQTL in 6 (q < 0.05)
• Constraint (gnomAD): pLI 0.00 (LoF-tolerant), LOEUF 1.18 (unconstrained)
• MANE Select transcript: NM_017832
• Notable: 59 clinical variants but no curated precision-oncology (CIViC) evidence yet

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: 17 — 13 protein_coding, 3 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

MANE Select: ENST00000322940

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

ENST00000322940, ENST00000374624, ENST00000445175, ENST00000466200, ENST00000899979, ENST00000919245, ENST00000964591, ENST00000964592, ENST00000998348, ENST00000998349, ENST00001097226, ENST00001123745, ENST00001123746, ENST00001128382, ENST00001128383, ENST00001128384, ENST00001139172

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.

Highest expression (Bgee): bronchial epithelial cell, tongue squamous epithelium, epithelium of bronchus, bronchus, hair follicle.

Genetic regulation across tissues (GTEx eQTL / sQTL)

ABITRAM is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 27 tissues and its splicing (sQTL) in 6 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

showing 20 of 33 significant tissue × QTL associations:

Tissue	QTL	q-value	Slope	Lead variant
Cells Cultured fibroblasts	eqtl	5.2e-15	-0.28	9:108934109:G:C
Skin Not Sun Exposed Suprapubic	eqtl	1.2e-11	-0.19	9:108943221:A:C
Muscle Skeletal	eqtl	2.4e-10	+0.14	9:108914840:T:C
Skin Sun Exposed Lower leg	eqtl	7.2e-10	-0.16	9:108943221:A:C
Whole Blood	eqtl	1.0e-09	+0.12	9:108916148:T:A
Adipose Subcutaneous	eqtl	5.9e-08	-0.20	9:108934109:G:C
Artery Aorta	eqtl	1.2e-07	-0.51	9:108986527:G:C
Artery Tibial	eqtl	7.6e-07	-0.34	9:108998922:G:A
Lung	eqtl	2.5e-06	-0.26	9:108986527:G:C
Thyroid	eqtl	2.9e-06	+0.17	9:108885484:C:T
Adipose Visceral Omentum	eqtl	4.9e-06	+0.20	9:108914840:T:C
Adipose Subcutaneous	sqtl	2.0e-05	-0.33	9:108966438:C:T
Nerve Tibial	eqtl	3.2e-05	+0.22	9:109055674:AC:A
Liver	eqtl	8.6e-05	-0.91	9:108869463:G:C
Testis	eqtl	1.3e-04	-0.14	9:109000645:C:T
Esophagus Gastroesophageal Junction	eqtl	2.1e-04	+0.22	9:108983817:T:G
Brain Cerebellum	eqtl	2.5e-04	-0.54	9:108962639:G:C
Breast Mammary Tissue	eqtl	3.8e-04	-0.18	9:108950644:G:C
Thyroid	sqtl	7.2e-04	+0.30	9:109120449:T:G
Heart Atrial Appendage	eqtl	1.5e-03	-0.44	9:108962639:G:C

FANTOM5 promoters

1 alternative TSS:

Promoter ID	TPM avg	Samples expressed
97930	9.5280	1770

Top tissues by expression

showing 100 of 288 tissues 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
cardia of stomach	UBERON:0001162	90.03	gold quality
vena cava	UBERON:0004087	89.80	gold quality
cervix epithelium	UBERON:0004801	89.79	gold quality
thyroid gland	UBERON:0002046	89.73	gold quality
choroid plexus epithelium	UBERON:0003911	89.69	gold quality
mammalian vulva	UBERON:0000997	89.62	gold quality
cauda epididymis	UBERON:0004360	89.61	gold quality
skin of leg	UBERON:0001511	89.05	gold quality
skin of abdomen	UBERON:0001416	89.03	gold quality
lateral globus pallidus	UBERON:0002476	88.96	gold quality
right lobe of thyroid gland	UBERON:0001119	88.93	gold quality
nucleus accumbens	UBERON:0001882	88.85	gold quality
caudate nucleus	UBERON:0001873	88.79	gold quality
putamen	UBERON:0001874	88.65	gold quality
CA1 field of hippocampus	UBERON:0003881	88.57	gold quality
zone of skin	UBERON:0000014	88.38	gold quality
pituitary gland	UBERON:0000007	88.30	gold quality
superficial temporal artery	UBERON:0001614	88.24	gold quality
middle temporal gyrus	UBERON:0002771	88.19	gold quality
subthalamic nucleus	UBERON:0001906	88.11	gold quality
esophagus mucosa	UBERON:0002469	88.08	gold quality
epithelium of mammary gland	UBERON:0003244	88.06	gold quality
rectum	UBERON:0001052	88.04	gold quality
dorsal plus ventral thalamus	UBERON:0001897	88.03	gold quality
mammary duct	UBERON:0001765	87.92	gold quality
oral cavity	UBERON:0000167	87.84	gold quality
lower lobe of lung	UBERON:0008949	87.83	gold quality
epithelial cell of pancreas	CL:0000083	87.76	gold quality
substantia nigra	UBERON:0002038	87.71	gold quality
diaphragm	UBERON:0001103	87.69	gold quality
Brodmann (1909) area 23	UBERON:0013554	87.65	gold quality
adenohypophysis	UBERON:0002196	87.64	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	87.61	gold quality
midbrain	UBERON:0001891	87.60	gold quality
superior vestibular nucleus	UBERON:0007227	87.57	gold quality
pons	UBERON:0000988	87.50	gold quality
amniotic fluid	UBERON:0000173	87.44	gold quality
spinal cord	UBERON:0002240	87.42	gold quality
body of pancreas	UBERON:0001150	87.36	gold quality
endometrium	UBERON:0001295	87.35	gold quality
type B pancreatic cell	CL:0000169	87.23	silver quality
jejunal mucosa	UBERON:0000399	87.22	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	87.18	gold quality
substantia nigra pars compacta	UBERON:0001965	87.16	gold quality
left ovary	UBERON:0002119	87.14	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	87.11	gold quality
uterine cervix	UBERON:0000002	87.10	gold quality
substantia nigra pars reticulata	UBERON:0001966	87.07	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	87.07	gold quality
tibial nerve	UBERON:0001323	86.99	gold quality
penis	UBERON:0000989	86.87	gold quality
vastus lateralis	UBERON:0001379	86.87	gold quality
hypothalamus	UBERON:0001898	86.87	gold quality
olfactory bulb	UBERON:0002264	86.87	silver quality
esophagus	UBERON:0001043	86.85	gold quality
Brodmann (1909) area 9	UBERON:0013540	86.84	gold quality
pharyngeal mucosa	UBERON:0000355	86.82	gold quality
forebrain	UBERON:0001890	86.81	gold quality
biceps brachii	UBERON:0001507	86.78	gold quality
endothelial cell	CL:0000115	86.77	silver quality
lower esophagus mucosa	UBERON:0035834	86.70	gold quality
telencephalon	UBERON:0001893	86.68	gold quality
right ovary	UBERON:0002118	86.68	gold quality
uterus	UBERON:0000995	86.67	gold quality
right adrenal gland	UBERON:0001233	86.66	gold quality
cingulate cortex	UBERON:0003027	86.66	gold quality
body of uterus	UBERON:0009853	86.66	gold quality
anterior cingulate cortex	UBERON:0009835	86.65	gold quality
prefrontal cortex	UBERON:0000451	86.64	gold quality
upper arm skin	UBERON:0004263	86.58	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

HPA expression

RNA tissue specificity: Low tissue specificity

showing 60 of 79 HPA tissues / cells by nTPM:

Tissue / cell	Axis	nTPM	Protein (IHC)
Cerebral cortex	tissue	25.4	low
Occipital cortex	tissue	25.4
Putamen	tissue	24.7
Somatosensory cortex	tissue	24.6
Epididymis	tissue	23.7	medium
Skin 1	tissue	23.0	medium
Prefrontal cortex	tissue	22.9
Basal ganglia	tissue	22.9	low
Retina	tissue	22.8
Parathyroid gland	tissue	21.8	low
Motor cortex	tissue	21.8
Hippocampal formation	tissue	21.7
Temporal cortex	tissue	20.6
Pons	tissue	20.4
Ventral forebrain	tissue	20.4
Choroid plexus	tissue	20.3
Midbrain	tissue	20.3
Postcentral gyrus	tissue	20.3
Entorhinal cortex	tissue	20.3
Thalamus	tissue	20.2
Fallopian tube	tissue	20.2	not detected
Nucleus accumbens	tissue	19.9
Superior colliculi	tissue	19.9
Retrosplenial and cingulate cortex	tissue	19.5
Testis	tissue	18.9	low
Medulla oblongata	tissue	18.7
Septum	tissue	18.6
Retrosplenial cortex	tissue	18.3
Spinal cord	tissue	18.2
Thyroid gland	tissue	17.7	not detected
Olfactory bulb	tissue	17.7
Insular cortex	tissue	17.1
Substantia nigra	tissue	16.8
Periaqueductal gray	tissue	16.5
Breast	tissue	16.1	medium
Hypothalamus	tissue	15.6
Esophagus	tissue	15.5	low
Amygdala	tissue	15.3
Rectum	tissue	15.1	medium
Pituitary gland	tissue	15.0
Heart muscle	tissue	14.7	medium
Bone marrow	tissue	14.7	low
Locus coeruleus	tissue	14.5
Salivary gland	tissue	14.4	low
Hippocampus	tissue	14.0	not detected
Colon	tissue	13.9	low
Stomach 1	tissue	13.7	medium
Liver	tissue	13.7	medium
Corpus callosum	tissue	13.6
Duodenum	tissue	13.5	medium
Seminal vesicle	tissue	13.4	medium
Adipose tissue	tissue	13.3	not detected
Cerebellum	tissue	13.2	low
Endometrium 1	tissue	12.7	not detected
Kidney	tissue	12.7	low
Vagina	tissue	12.5	medium
Pancreas	tissue	12.5	medium
Skeletal muscle	tissue	12.3	medium
Small intestine	tissue	12.3	medium
Lung	tissue	11.9	low

Brain sub-regions (HPA Brain Atlas): detected in 190; highest nTPM — Dorsal hippocampus (21.7), Ventral hippocampus (21.1), Temporo-occipital transitional zone (20.7), Subiculum (20.4), Caudate nucleus (19.9).

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

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

showing 30 of 59 miRNAs:

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

Functional genomics

gnomAD constraint: pLI 8.06e-05, LOEUF 1.18, missense Z 0.191 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD

Regional missense constraint (gnomAD RMC): no regional variation along ENST00000322940 — one region, missense o/e 0.98.

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

Mouse-model phenotypes

Observed phenotypes of the mouse ortholog (MGI:2677850) from MGI (Alliance of Genome Resources) — knockout/mutant phenotypes, ranked by annotation count. 4 distinct phenotype terms.

Mouse phenotype (MP)	Records
abnormal retina vasculature morphology	1
increased cardiac muscle contractility	1
increased bone mineral content	1
decreased total retina thickness	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
Pongo abelii	Q5RFS0	100.0%	Diamond
Xenopus tropicalis	Q28G67	90.2%	Diamond
Xenopus laevis	Q6GR35	90.2%	Diamond
Bos taurus	Q29S16	89.8%	Diamond
Gallus gallus	Q5ZHW7	80.8%	Diamond
Dictyostelium discoideum	Q54TD9	36.8%	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
TMEM245	protein-coding	23731
FRRS1L	protein-coding	23732
MIR32	ncRNA	407036
ELP1	protein-coding	8518
CTNNAL1	protein-coding	8727
ACTL7B	protein-coding	10880
ACTL7A	protein-coding	10881
EPB41L4B	protein-coding	54566

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

Predicted structure (AlphaFold)

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

Human Protein Atlas

Protein class: Predicted intracellular proteins, Plasma proteins

Protein evidence: Evidence at protein level

Subcellular location (HPA, imaging): cytosol; nucleoplasm; cytokinetic bridge; kinetochore; mitotic spindle; primary cilium; primary cilium tip

Antibody reliability (HPA): IH uncertain · IF approved

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: 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 (6): nucleus (GO:0005634), nuclear speck (GO:0016607), lamellipodium (GO:0030027), dendrite (GO:0030425), growth cone (GO:0030426), filopodium tip (GO:0032433)

GO top-level categories

22 GO namespaces:

Category	Terms
actin binding	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
cellular anatomical structure	1

Protein interactions and networks

STRING

showing 15 of 577 interactions by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ABITRAM	FRRS1L	Q9P0K9	882
ABITRAM	HSDL1	Q3SXM5	512
ABITRAM	CTNNAL1	Q9UBT7	507
ABITRAM	SPRYD7	Q5W111	469
ABITRAM	NIPAL3	Q6P499	465
ABITRAM	SERAC1	Q96JX3	459
ABITRAM	NIPAL1	Q6NVV3	454
ABITRAM	NHERF4	Q86UT5	447
ABITRAM	ZACN	Q401N2	445
ABITRAM	TMEM245	Q9H330	441
ABITRAM	ELP1	O95163	441
ABITRAM	C8A	P07357	437
ABITRAM	AMZ2	Q86W34	433
ABITRAM	LGALS8	O00214	420
ABITRAM	C8B	P07358	388

IntAct

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

6 partners by confidence:

Partner	Interaction type	MIscore	Records
PUS10	physical association	0.740	6
HMBOX1	physical association	0.720	6
MESD	physical association	0.560	3
PGCKA1	physical association	0.560	3
POTEF	association	0.530	2
FYN	association	0.350	1

Disease & clinical

Genetic variants

Variant evidence for ABITRAM: 59 ClinVar records (1 pathogenic / likely pathogenic). Per-variant detail is on Sugi Variant.

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	1
Uncertain significance	45
Likely benign	1
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
1527542	GRCh37/hg19 9q31.2-32(chr9:109265628-117650999)x1	Likely pathogenic	criteria provided, single submitter	1

Per-variant reference — Sugi Variant

Explore ABITRAM’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; 42 predictions of 419):

Position(s)	Effect	Δscore	Sites
9:108934566–108934567	donor_loss	1.0000	5
9:108939193	acceptor_gain	1.0000
9:108939547–108939548	acceptor_loss	1.0000	4
9:108939194–108939195	acceptor_loss	0.9900	6
9:108939273–108939274	donor_loss	0.9900	5
9:108939383–108939384	acceptor_loss	0.9900	6
9:108939455–108939456	donor_loss	0.9900	6
9:108939547–108939548	acceptor_loss	0.9900	2
9:108936384	donor_gain	0.9800
9:108936306–108936307	acceptor_loss	0.9700	6

AlphaMissense

552 missense substitutions predicted likely pathogenic (of 1,180 scored), across 125 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
H41	8	0.997	0.999
D35	8	0.984	0.995
N43	8	0.975	0.999
H54	8	0.971	0.995
N79	8	0.967	0.998
N123	8	0.946	0.995
F20	7	0.987	0.995
E121	7	0.974	0.995
F91	7	0.971	0.996
Q90	7	0.962	0.994
K86	7	0.961	1.000
C99	7	0.948	0.998
C46	7	0.933	0.997
W23	7	0.921	0.970
C74	7	0.881	0.974
E152	7	0.869	0.973
Q40	7	0.863	0.992
C37	7	0.862	0.975
D27	7	0.794	0.920
G83	6	0.998	1.000

HPA cancer prognostics

RNA cancer specificity: Low cancer specificity

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

2 prognostic cancer types:

Cancer	Prognostic	p-value
Liver Hepatocellular Carcinoma (TCGA)	unfavorable	0.000246
Kidney Renal Clear Cell Carcinoma (TCGA)	favorable	0.00031

Disease associations

OMIM: gene MIM:620392 | disease phenotypes:

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (CPIC guideline: no)

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)

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

10 trials:

NCT	Phase	Status	Title
NCT01064505	Phase 1	COMPLETED	Safety Study of a Single IVT Injection of QPI-1007 in Chronic Optic Nerve Atrophy and Recent Onset NAION Patients
NCT05147701	Phase 1	RECRUITING	Safety of Cultured Allogeneic Adult Umbilical Cord Derived Mesenchymal Stem Cells for NAION
NCT02882477	Phase 2/3	UNKNOWN	Treatment of Wolfram Syndrome Type 2 With the Chelator Deferiprone and Incretin Based Therapy
NCT01834079	Phase 1/2	UNKNOWN	Study the Safety and Efficacy of Bone Marrow Derived Autologous Cells for the Treatment of Optic Nerve Disease
NCT04680143	Phase 1/2	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