ABLIM1

Summary

ABLIM1 (actin binding LIM protein 1, HGNC:78) is a protein-coding gene on chromosome 10q25.3, encoding Actin-binding LIM protein 1 (O14639). May act as scaffold protein.

This gene encodes a LIM zinc-binding domain-containing protein that binds to actin filaments and mediates interactions between actin and cytoplasmic targets. Alternatively spliced transcript variants encoding different isoforms have been identified.

Source: NCBI Gene 3983 — RefSeq curated summary.

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 161 total — 9 pathogenic, 2 likely-pathogenic
• MANE Select transcript: NM_002313

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:78
Approved symbol	ABLIM1
Name	actin binding LIM protein 1
Location	10q25.3
Locus type	gene with protein product
Status	Approved
Aliases	abLIM, limatin
Ensembl gene	ENSG00000099204
Ensembl biotype	protein_coding
OMIM	602330
Entrez	3983

Gene structure

Transcript identifiers

Ensembl transcripts: 15 — 11 protein_coding, 3 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000369253, ENST00000369256, ENST00000392952, ENST00000392955, ENST00000428430, ENST00000440467, ENST00000466400, ENST00000477638, ENST00000481974, ENST00000485570, ENST00000533213, ENST00000649363, ENST00000651023, ENST00000651092, ENST00000707119

RefSeq mRNA: 26 — MANE Select: NM_002313 NM_001003407, NM_001322882, NM_001322883, NM_001322884, NM_001322885, NM_001322886, NM_001322887, NM_001322888, NM_001322889, NM_001322890, NM_001322891, NM_001322892, NM_001322893, NM_001322894, NM_001322895, NM_001322896, NM_001322897, NM_001322898, NM_001322899, NM_001322900, NM_001352440, NM_001352441, NM_001352442, NM_001352443, NM_002313, NM_006720

CCDS: CCDS31288, CCDS31289, CCDS7590, CCDS81508, CCDS81509

Canonical transcript exons

ENST00000533213 — 23 exons

Exon	Start	End
ENSE00000811956	114453379	114453483
ENSE00000811965	114472977	114473132
ENSE00000811969	114473879	114473956
ENSE00000933328	114441722	114441786
ENSE00000933329	114444029	114444134
ENSE00000933330	114445312	114445403
ENSE00000933331	114447880	114448020
ENSE00000933333	114487958	114488016
ENSE00000986769	114465698	114465827
ENSE00001000257	114468181	114468216
ENSE00001435390	114441017	114441077
ENSE00001548840	114451624	114451671
ENSE00001647651	114657957	114658275
ENSE00001692782	114545005	114545098
ENSE00001714043	114547650	114547776
ENSE00001754905	114575416	114575599
ENSE00002474216	114440082	114440089
ENSE00003480415	114491791	114491878
ENSE00003519304	114439176	114439250
ENSE00003652169	114601827	114601961
ENSE00003692120	114571297	114571406
ENSE00003716256	114437844	114437924
ENSE00003751361	114431112	114436373

Expression profiles

Bgee: expression breadth ubiquitous, 299 present calls, max score 99.68.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 43.3008 / max 1062.0015, expressed in 1510 samples.

FANTOM5 promoters (32 alternative TSS)

Promoter ID	TPM avg	Samples expressed
111487	11.3703	931
111486	9.1239	1011
111511	6.5644	861
111485	6.0737	744
111495	3.2110	775
111496	1.4767	357
111505	1.3655	344
111484	1.1413	305
111497	0.4229	124
111506	0.3578	147

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left ventricle myocardium	UBERON:0006566	99.68	gold quality
esophagus squamous epithelium	UBERON:0006920	99.63	gold quality
cerebellar vermis	UBERON:0004720	99.56	gold quality
cardiac muscle of right atrium	UBERON:0003379	99.47	gold quality
epithelium of esophagus	UBERON:0001976	99.46	gold quality
myocardium	UBERON:0002349	99.34	gold quality
heart right ventricle	UBERON:0002080	99.24	gold quality
pharyngeal mucosa	UBERON:0000355	99.23	gold quality
cerebellum	UBERON:0002037	99.22	gold quality
cerebellar cortex	UBERON:0002129	99.20	gold quality
cerebellar hemisphere	UBERON:0002245	99.19	gold quality
squamous epithelium	UBERON:0006914	99.16	gold quality
parotid gland	UBERON:0001831	99.14	gold quality
gingiva	UBERON:0001828	99.11	gold quality
lower esophagus mucosa	UBERON:0035834	99.06	gold quality
gingival epithelium	UBERON:0001949	99.05	gold quality
oral cavity	UBERON:0000167	99.00	gold quality
right hemisphere of cerebellum	UBERON:0014890	98.99	gold quality
gluteal muscle	UBERON:0002000	98.97	gold quality
paraflocculus	UBERON:0005351	98.97	gold quality
apex of heart	UBERON:0002098	98.95	gold quality
body of tongue	UBERON:0011876	98.93	gold quality
synovial joint	UBERON:0002217	98.88	gold quality
tongue	UBERON:0001723	98.86	gold quality
cardiac ventricle	UBERON:0002082	98.86	gold quality
superior surface of tongue	UBERON:0007371	98.85	gold quality
heart left ventricle	UBERON:0002084	98.84	gold quality
upper arm skin	UBERON:0004263	98.79	gold quality
nipple	UBERON:0002030	98.77	gold quality
penis	UBERON:0000989	98.69	gold quality

Single-cell (SCXA)

Detected in 10 experiment(s), a significant marker in 6.

Experiment	Marker?	Max mean expression
E-HCAD-35	yes	91.10
E-GEOD-134144	yes	30.45
E-HCAD-25	yes	21.75
E-HCAD-10	yes	13.18
E-GEOD-84465	yes	12.10
E-MTAB-10283	no	259.21
E-MTAB-8381	no	218.71
E-MTAB-7249	no	206.37
E-CURD-53	no	174.25
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

172 targeting ABLIM1, 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-8485	100.00	77.57	4731
HSA-MIR-450A-1-3P	100.00	69.33	1837
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-574-5P	100.00	66.01	989
HSA-MIR-4776-3P	100.00	68.73	1340
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-3667-3P	99.99	67.17	1636
HSA-MIR-3185	99.99	68.12	1959
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-3688-3P	99.97	72.02	2834
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-551B-5P	99.96	71.28	3493
HSA-MIR-1468-3P	99.96	72.74	3797
HSA-MIR-4267	99.96	66.53	2368
HSA-MIR-651-3P	99.94	73.48	5177
HSA-MIR-1236-3P	99.94	68.04	1695
HSA-MIR-9983-3P	99.94	71.48	3631
HSA-MIR-6835-3P	99.93	70.49	2904
HSA-MIR-6768-5P	99.92	67.36	1942
HSA-MIR-515-5P	99.92	69.82	2343
HSA-MIR-519E-5P	99.92	69.62	2358
HSA-MIR-6809-3P	99.91	71.45	3814
HSA-MIR-4753-3P	99.90	71.03	3786

Literature-anchored findings (GeneRIF, showing 7)

• SNP rs727532 in ABLIM1 (10q25) had significant association in the multivariate test & strong associations with novelty seeking, harm avoidance, reward dependence and alcohol dependence in the COGA sample. (PMID:21547531)
• Exon 11 inclusion isoform of ABLIM1 may have a muscle-specific function, and its abnormal splicing could be related to muscle symptoms of myotonic dystrophy type 1. (PMID:25403273)
• Rictor promotes cell migration and actin polymerization through regulating ABLIM1 phosphorylation in Hepatocellular Carcinoma. (PMID:33061800)
• Effect and in silico characterization of genetic variants associated with severe spermatogenic disorders in a large Iberian cohort. (PMID:33784440)
• Actin-Binding LIM 1 (ABLIM1) Inhibits Glioblastoma Progression and Serves as a Novel Prognostic Biomarker. (PMID:36583064)
• ABLIM1, a novel ubiquitin E3 ligase, promotes growth and metastasis of colorectal cancer through targeting IkBalpha ubiquitination and activating NF-kB signaling. (PMID:38228802)
• Spitz melanoma with MAP3K8::ABLIM1 rearrangement: a case report with review of the literature. (PMID:39363234)

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	ablim1b	ENSDARG00000045064
danio_rerio	ablim1a	ENSDARG00000060149
mus_musculus	Ablim1	ENSMUSG00000025085
rattus_norvegicus	AABR07007032.1	ENSRNOG00000046333
drosophila_melanogaster	Unc-115a	FBGN0051352
drosophila_melanogaster	Unc-115b	FBGN0260463

Paralogs (3): DMTN (ENSG00000158856), ABLIM2 (ENSG00000163995), ABLIM3 (ENSG00000173210)

Protein

Protein identifiers

Actin-binding LIM protein 1 — O14639 (reviewed: O14639)

Alternative names: Actin-binding LIM protein family member 1, Actin-binding double zinc finger protein, LIMAB1, Limatin

All UniProt accessions (8): O14639, A0A3B3IS55, A0A494C1P1, A0A9L9PY99, B7Z4H1, F6XFR5, F8W8M4, H0Y7N6

UniProt curated annotations — full annotation on UniProt →

Function. May act as scaffold protein. May play a role in the development of the retina. Has been suggested to play a role in axon guidance.

Subunit / interactions. Binds F-actin. Interacts with ABRA.

Subcellular location. Cytoplasm. Cytoskeleton.

Tissue specificity. Detected in liver, heart, skeletal muscle, brain and retina, where it is concentrated in the inner segment and in the outer plexiform layers.

Isoforms (6)

UniProt ID	Names	Canonical?
O14639-1	1	yes
O14639-2	2
O14639-3	3
O14639-4	4
O14639-5	5
O14639-6	6

RefSeq proteins (26): NP_001003407, NP_001309811, NP_001309812, NP_001309813, NP_001309814, NP_001309815, NP_001309816, NP_001309817, NP_001309818, NP_001309819, NP_001309820, NP_001309821, NP_001309822, NP_001309823, NP_001309824, NP_001309825, NP_001309826, NP_001309827, NP_001309828, NP_001309829, NP_001339369, NP_001339370, NP_001339371, NP_001339372, NP_002304, NP_006711 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001781	Znf_LIM	Domain
IPR003128	Villin_headpiece	Domain
IPR032402	AbLIM_anchor	Domain
IPR036886	Villin_headpiece_dom_sf	Homologous_superfamily
IPR051618	Actin-binding_LIM	Family

Pfam: PF00412, PF02209, PF16182

UniProt features (45 total): modified residue 19, splice variant 6, domain 5, sequence conflict 4, compositionally biased region 3, region of interest 3, sequence variant 2, chain 1, cross-link 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-O14639-F1	59.86	0.19

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 (20): 216, 367, 373, 396, 422, 426, 431, 433, 435, 439, 452, 455, 458, 498, 587, 640, 655, 677, 706, 620

Function

Pathways and Gene Ontology

Reactome pathways

5 pathways

ID	Pathway
R-HSA-418885	DCC mediated attractive signaling
R-HSA-1266738	Developmental Biology
R-HSA-373752	Netrin-1 signaling
R-HSA-422475	Axon guidance
R-HSA-9675108	Nervous system development

MSigDB gene sets: 372 (showing top): VERHAAK_AML_WITH_NPM1_MUTATED_DN, MODULE_93, YAATNRNNNYNATT_UNKNOWN, CHIARADONNA_NEOPLASTIC_TRANSFORMATION_KRAS_DN, JAEGER_METASTASIS_DN, ZHAN_MULTIPLE_MYELOMA_MF_UP, GOZGIT_ESR1_TARGETS_DN, HSIAO_HOUSEKEEPING_GENES, LINDGREN_BLADDER_CANCER_CLUSTER_3_DN, AP4_Q6, GOBP_NEUROGENESIS, CHEOK_RESPONSE_TO_HD_MTX_UP, CAGCTG_AP4_Q5, MONNIER_POSTRADIATION_TUMOR_ESCAPE_UP, SENESE_HDAC1_AND_HDAC2_TARGETS_DN

GO Biological Process (8): transcription by RNA polymerase II (GO:0006366), cytoskeleton organization (GO:0007010), axon guidance (GO:0007411), visual perception (GO:0007601), animal organ morphogenesis (GO:0009887), lamellipodium assembly (GO:0030032), positive regulation of transcription by RNA polymerase II (GO:0045944), cilium assembly (GO:0060271)

GO Molecular Function (4): actin binding (GO:0003779), metal ion binding (GO:0046872), actin filament binding (GO:0051015), protein binding (GO:0005515)

GO Cellular Component (6): stress fiber (GO:0001725), cytoplasm (GO:0005737), postsynaptic density (GO:0014069), actin cytoskeleton (GO:0015629), lamellipodium (GO:0030027), cytoskeleton (GO:0005856)

Reactome top-level categories

Rollup of top-4 pathways:

Category	Pathways
Netrin-1 signaling	1
Axon guidance	1
Nervous system development	1
Developmental Biology	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
plasma membrane bounded cell projection assembly	2
DNA-templated transcription	1
organelle organization	1
axonogenesis	1
neuron projection guidance	1
sensory perception of light stimulus	1
anatomical structure morphogenesis	1
animal organ development	1
lamellipodium organization	1
regulation of transcription by RNA polymerase II	1
transcription by RNA polymerase II	1
positive regulation of DNA-templated transcription	1
axoneme assembly	1
intraciliary transport involved in cilium assembly	1
cilium organization	1
protein localization to cilium	1
organelle assembly	1
trans-Golgi to periciliary membrane compartment transport	1
ciliary transition zone assembly	1
cytoskeletal protein binding	1
cation binding	1
actin binding	1
protein-containing complex binding	1
binding	1
actomyosin	1
contractile actin filament bundle	1
intracellular anatomical structure	1
cellular anatomical structure	1
asymmetric synapse	1
postsynaptic specialization	1
cytoskeleton	1
cell leading edge	1
plasma membrane bounded cell projection	1
intracellular membraneless organelle	1

Protein interactions and networks

STRING

1148 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ABLIM1	ABRA	Q8N0Z2	853
ABLIM1	SRF	P11831	680
ABLIM1	FSCN1	Q16658	671
ABLIM1	DCAF7	P61962	552
ABLIM1	TTN	Q8WZ42	512
ABLIM1	KCNJ12	Q14500	494
ABLIM1	CELF1	Q92879	481
ABLIM1	EPHB1	P54762	467
ABLIM1	CLCN1	P35523	461
ABLIM1	NEXN	Q0ZGT2	451
ABLIM1	FOSL2	P15408	430
ABLIM1	NHLRC2	Q8NBF2	424
ABLIM1	VWA2	Q5GFL6	422
ABLIM1	DPYSL5	Q9BPU6	421
ABLIM1	NCLN	Q969V3	415

IntAct

178 interactions, top by confidence:

A	B	Type	Score
MED21	MED19	psi-mi:“MI:0914”(association)	0.880
YWHAH	ABLIM1	psi-mi:“MI:0914”(association)	0.800
ABLIM1	YWHAZ	psi-mi:“MI:0915”(physical association)	0.790
ABLIM1	YWHAE	psi-mi:“MI:0915”(physical association)	0.650
NCBP2	KPNA3	psi-mi:“MI:0914”(association)	0.640
YWHAG	BLTP3B	psi-mi:“MI:0914”(association)	0.640
YWHAG	BLTP3B	psi-mi:“MI:2364”(proximity)	0.640
SFN	ABLIM1	psi-mi:“MI:0915”(physical association)	0.630
ABLIM1	SFN	psi-mi:“MI:0915”(physical association)	0.630
YWHAH	PLEKHG3	psi-mi:“MI:0914”(association)	0.610
YWHAB	BLTP3B	psi-mi:“MI:2364”(proximity)	0.610
YWHAB	BLTP3B	psi-mi:“MI:0914”(association)	0.610
YWHAE	PIK3C2A	psi-mi:“MI:0914”(association)	0.570
YWHAH	BLTP3B	psi-mi:“MI:0914”(association)	0.570
YWHAH	BLTP3B	psi-mi:“MI:2364”(proximity)	0.570
CARD9	ABLIM1	psi-mi:“MI:0915”(physical association)	0.560
ABLIM1	CARD9	psi-mi:“MI:0915”(physical association)	0.560
YWHAG	SHTN1	psi-mi:“MI:0914”(association)	0.560
YWHAQ	IGLC7	psi-mi:“MI:0914”(association)	0.530
YWHAB	SHTN1	psi-mi:“MI:0914”(association)	0.530
YWHAE	SHTN1	psi-mi:“MI:0914”(association)	0.530
YWHAZ	SHTN1	psi-mi:“MI:0914”(association)	0.530
YWHAZ	BLTP3B	psi-mi:“MI:0914”(association)	0.530
KLHL40	CBX4	psi-mi:“MI:0914”(association)	0.530
CYB5D2	ABLIM1	psi-mi:“MI:0914”(association)	0.530
LIN7C	ABLIM1	psi-mi:“MI:0914”(association)	0.530
MPP2	ABLIM1	psi-mi:“MI:0914”(association)	0.530

BioGRID (250): CARD9 (Two-hybrid), ABLIM1 (Affinity Capture-MS), ABLIM1 (Affinity Capture-MS), ABLIM1 (Affinity Capture-MS), ABLIM1 (Affinity Capture-MS), ABLIM1 (Affinity Capture-MS), NMT1 (Affinity Capture-MS), SEPSECS (Affinity Capture-MS), VIM (Two-hybrid), ABLIM1 (Affinity Capture-MS), ABLIM1 (Two-hybrid), BEGAIN (Two-hybrid), TRAF2 (Two-hybrid), LDOC1 (Two-hybrid), TSC22D4 (Two-hybrid)

ESM2 similar proteins: A0M8U1, A6H6W9, A6QL63, F1LSG8, O14639, P42229, P42230, P42232, P51692, P52632, P97875, Q12800, Q13330, Q1RLU8, Q2PG42, Q4V860, Q5RAN1, Q5RBB8, Q5ZKV9, Q62599, Q6AYJ2, Q6GQW0, Q6NRB5, Q6NZH6, Q6ZUT9, Q78E65, Q7T2U9, Q7Z6J6, Q8BR65, Q8CI71, Q8K4B0, Q8K4G5, Q8K4Q0, Q8N122, Q8R3S6, Q8WYK2, Q95115, Q9D2N4, Q9ERA0, Q9H7L9

Diamond homologs: A0JNI8, A2I8Z7, A2PZF9, G5EC36, G5EE86, O14639, O35652, O60663, O88609, O94929, O97581, P20154, P25791, P25800, P25801, P29673, P29674, P34764, P34765, P36198, P36200, P37137, P48742, P50211, P50212, P50458, P50480, P50481, P52889, P53405, P53406, P53407, P53408, P53409, P53410, P53411, P53412, P53413, P53667, P53668

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 160 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Activation of BAD and translocation to mitochondria	7	49.4×	8e-09
Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex	7	43.5×	2e-08
SARS-CoV-1 targets host intracellular signalling and regulatory pathways	7	43.5×	2e-08
Activation of BH3-only proteins	7	32.2×	1e-07
RHO GTPases activate PKNs	9	26.4×	8e-09
Dopamine Neurotransmitter Release Cycle	5	23.0×	8e-05
Intrinsic Pathway for Apoptosis	8	21.7×	2e-07
RHO GTPases activate IQGAPs	5	16.0×	4e-04

GO biological processes:

GO term	Partners	Fold	FDR
protein targeting	5	13.9×	6e-03
epidermal growth factor receptor signaling pathway	6	11.3×	4e-03
intracellular protein localization	14	11.1×	5e-08
cell migration	13	6.1×	2e-04
in utero embryonic development	11	6.0×	1e-03
cilium assembly	10	5.6×	4e-03
positive regulation of gene expression	13	3.8×	7e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	9
Likely pathogenic	2
Uncertain significance	117
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (11)

Variant ID	HGVS	Classification
144206	GRCh38/hg38 10q25.1-26.3(chr10:108102587-133620674)x3	Pathogenic
1527605	GRCh37/hg19 10q25.1-26.3(chr10:108455687-135427143)	Pathogenic
2671974	GRCh37/hg19 10q25.1-26.3(chr10:111378692-135427143)x3	Pathogenic
443838	GRCh37/hg19 10q25.1-26.3(chr10:106003533-135427143)x3	Pathogenic
563801	GRCh37/hg19 10q24.33-26.3(chr10:105613040-135427143)x3	Pathogenic
57171	GRCh38/hg38 10q25.3(chr10:114584882-117015907)x1	Pathogenic
57507	GRCh38/hg38 10q25.2-26.3(chr10:111313099-133620674)x3	Pathogenic
625657	GRCh37/hg19 10q25.1-26.3(chr10:110022170-135439095)	Pathogenic
687114	GRCh37/hg19 10q25.2-26.3(chr10:114544537-135427143)x3	Pathogenic
151000	GRCh38/hg38 10q25.2-25.3(chr10:110804735-114884010)x1	Likely pathogenic
3063162	GRCh37/hg19 10q25.1-26.13(chr10:107129993-123817654)x3	Likely pathogenic

SpliceAI

4091 predictions. Top by Δscore:

Variant	Effect	Δscore
10:114441715:ATCTT:A	donor_loss	1.0000
10:114441716:TCTTA:T	donor_loss	1.0000
10:114441717:CTTAC:C	donor_loss	1.0000
10:114441718:TTA:T	donor_loss	1.0000
10:114441719:TACCC:T	donor_loss	1.0000
10:114441720:A:AC	donor_gain	1.0000
10:114441720:A:T	donor_loss	1.0000
10:114441720:AC:A	donor_gain	1.0000
10:114441721:C:CC	donor_gain	1.0000
10:114441721:CC:C	donor_gain	1.0000
10:114441782:TGAAG:T	acceptor_gain	1.0000
10:114441787:C:CC	acceptor_gain	1.0000
10:114441787:C:G	acceptor_loss	1.0000
10:114441788:T:A	acceptor_loss	1.0000
10:114441791:G:GC	acceptor_gain	1.0000
10:114444025:TTAC:T	donor_loss	1.0000
10:114444130:TTAAG:T	acceptor_gain	1.0000
10:114444131:TAAG:T	acceptor_gain	1.0000
10:114444132:AAG:A	acceptor_gain	1.0000
10:114444133:AG:A	acceptor_gain	1.0000
10:114444135:C:CC	acceptor_gain	1.0000
10:114444140:C:CT	acceptor_gain	1.0000
10:114444142:C:CT	acceptor_gain	1.0000
10:114450209:CA:C	acceptor_gain	1.0000
10:114451623:CCATG:C	donor_gain	1.0000
10:114465692:CCTTA:C	donor_loss	1.0000
10:114465693:CTTA:C	donor_loss	1.0000
10:114465694:TTA:T	donor_loss	1.0000
10:114465695:TAC:T	donor_loss	1.0000
10:114465696:A:AC	donor_gain	1.0000

AlphaMissense

4740 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
10:114436318:A:G	F760S	1.000
10:114473068:A:T	I395N	1.000
10:114473095:A:G	L386S	1.000
10:114487991:A:C	C336W	1.000
10:114487992:C:G	C336S	1.000
10:114487992:C:T	C336Y	1.000
10:114487993:A:G	C336R	1.000
10:114487993:A:T	C336S	1.000
10:114488000:A:C	H333Q	1.000
10:114488000:A:T	H333Q	1.000
10:114488001:T:C	H333R	1.000
10:114488002:G:C	H333D	1.000
10:114488003:C:A	W332C	1.000
10:114488003:C:G	W332C	1.000
10:114488005:A:G	W332R	1.000
10:114488005:A:T	W332R	1.000
10:114488007:A:T	V331D	1.000
10:114491796:A:G	L326P	1.000
10:114491802:A:C	M324R	1.000
10:114491802:A:G	M324T	1.000
10:114491812:C:G	G321R	1.000
10:114491812:C:T	G321R	1.000
10:114491819:G:C	F318L	1.000
10:114491819:G:T	F318L	1.000
10:114491820:A:C	F318C	1.000
10:114491820:A:G	F318S	1.000
10:114491821:A:C	F318V	1.000
10:114491821:A:G	F318L	1.000
10:114491821:A:T	F318I	1.000
10:114491831:G:C	C314W	1.000

dbSNP variants (sampled 300 via entrez): RS1000002460 (10:114459382 A>G), RS1000013098 (10:114499582 G>A), RS1000026487 (10:114432022 A>G), RS1000038982 (10:114606622 C>T), RS1000062320 (10:114719588 T>C), RS1000081923 (10:114760120 C>T), RS1000090342 (10:114649402 A>G), RS1000099231 (10:114760443 C>T), RS1000102362 (10:114546992 A>G), RS1000108738 (10:114716593 T>C,G), RS1000111168 (10:114511732 G>A), RS1000116060 (10:114690436 G>A,T), RS1000122173 (10:114558338 A>G,T), RS1000129536 (10:114737801 T>C,G), RS1000141329 (10:114670949 T>C)

Disease associations

OMIM: gene MIM:602330 | disease phenotypes:

GenCC curated gene-disease

Mondo (1): distal trisomy 10q (MONDO:0019884)

Orphanet (1): Distal duplication 10q syndrome (Orphanet:96102)

HPO phenotypes

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

GWAS associations

5 associations (top):

Study	Trait	p-value
GCST001762_388	Obesity-related traits	6.000000e-06
GCST005352_8	Paclitaxel disposition in epithelial ovarian cancer	2.000000e-06
GCST008021_2	Taste perception (total score including 6-n-propylthiouracil) in obesity with metabolic syndrome	9.000000e-06
GCST009391_1185	Metabolite levels	1.000000e-06
GCST009441_10	Age-related cognitive decline (memory) (slope of z-scores)	5.000000e-06

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0004340	body mass index
EFO:0021575	adipic acid measurement
EFO:0007710	cognitive decline measurement

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
C538087	Distal Trisomy 10q Syndrome (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
bisphenol A	increases expression	3
sodium arsenite	affects cotreatment, increases abundance, increases expression, decreases expression	3
Estradiol	affects expression, affects cotreatment, decreases expression	3
Tobacco Smoke Pollution	decreases expression, decreases methylation, increases expression	3
Cadmium Chloride	decreases expression, increases expression	3
(+)-JQ1 compound	decreases expression	2
Arsenic Trioxide	decreases response to substance, increases expression	2
Benzo(a)pyrene	increases methylation, increases mutagenesis	2
Doxorubicin	affects response to substance, decreases expression	2
Progesterone	affects cotreatment, decreases expression, increases expression	2
Smoke	decreases expression	2
Cyclosporine	decreases expression	2
GSK-J4	increases expression	1
FR900359	affects phosphorylation	1
TAK-243	increases sumoylation	1
triphenyl phosphate	affects expression	1
alpha-pinene	affects cotreatment, decreases expression, increases oxidation, increases abundance	1
deoxynivalenol	increases expression	1
pyrogallol 1,3-dimethyl ether	affects cotreatment, affects localization, increases expression	1
arsenite	affects binding, decreases reaction	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
manganese chloride	affects cotreatment, increases abundance, increases expression	1
potassium chromate(VI)	decreases expression	1
nickel sulfate	decreases expression	1
coumarin	affects phosphorylation	1
methacrylaldehyde	increases abundance, affects cotreatment, decreases expression, increases oxidation	1
beta-methylcholine	affects expression	1
perfluorooctane sulfonic acid	increases expression	1
seocalcitol	increases expression	1
CGP 52608	affects binding, increases reaction	1

Clinical trials (associated diseases)

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