BMS1

Summary

BMS1 (BMS1 ribosome biogenesis factor, HGNC:23505) is a protein-coding gene on chromosome 10q11.21, encoding Ribosome biogenesis protein BMS1 homolog (Q14692). GTPase required for the synthesis of 40S ribosomal subunits and for processing of pre-ribosomal RNA (pre-rRNA) at sites A0, A1, and A2. It is a common-essential gene (DepMap: required in 99.5% of cancer cell lines).

This gene likely encodes a ribosome assembly protein. A similar protein in yeast functions in 35S-rRNA processing, which includes a series of cleavage steps critical for formation of 40S ribosomes. Related pseudogenes exist on chromosomes 2, 9, 10, 15, 16, and 22.

Source: NCBI Gene 9790 — RefSeq curated summary.

At a glance

• Gene–disease (curated): aplasia cutis congenita (Strong, GenCC)
• GWAS associations: 2
• Clinical variants (ClinVar): 273 total — 1 pathogenic
• Phenotypes (HPO): 14
• Cancer dependency (DepMap): dependent in 99.5% of screened cell lines (common-essential)
• MANE Select transcript: NM_014753

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23505
Approved symbol	BMS1
Name	BMS1 ribosome biogenesis factor
Location	10q11.21
Locus type	gene with protein product
Status	Approved
Aliases	KIAA0187
Ensembl gene	ENSG00000165733
Ensembl biotype	protein_coding
OMIM	611448
Entrez	9790

Gene structure

Transcript identifiers

Ensembl transcripts: 15 — 15 protein_coding

ENST00000374518, ENST00000877422, ENST00000877423, ENST00000877424, ENST00000877425, ENST00000877426, ENST00000923311, ENST00000923314, ENST00000923315, ENST00000923316, ENST00000923317, ENST00000923318, ENST00000923319, ENST00000923320, ENST00000966891

RefSeq mRNA: 1 — MANE Select: NM_014753 NM_014753

CCDS: CCDS7199

Canonical transcript exons

ENST00000374518 — 23 exons

Exon	Start	End
ENSE00001095964	42796474	42797231
ENSE00001164869	42830261	42830422
ENSE00001164898	42820934	42820992
ENSE00001164918	42817318	42817494
ENSE00001164937	42802137	42802218
ENSE00001164945	42798468	42798625
ENSE00001164955	42797422	42797523
ENSE00001463708	42830866	42834937
ENSE00001463721	42782795	42782830
ENSE00001659114	42820236	42820424
ENSE00001686390	42816599	42816672
ENSE00001729985	42822062	42822184
ENSE00001736372	42823118	42823265
ENSE00002433289	42820508	42820688
ENSE00002438287	42792493	42792614
ENSE00002443089	42787168	42787247
ENSE00002474218	42793852	42793991
ENSE00002475799	42791627	42791769
ENSE00002482209	42823609	42823784
ENSE00002486183	42784362	42784570
ENSE00002499463	42790323	42790511
ENSE00002507543	42785482	42785672
ENSE00002527023	42792957	42793144

Expression profiles

Bgee: expression breadth ubiquitous, 287 present calls, max score 94.39.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 30.6885 / max 531.8351, expressed in 1812 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
104736	30.6885	1812

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
tendon of biceps brachii	UBERON:0008188	94.39	gold quality
body of tongue	UBERON:0011876	90.69	gold quality
pharyngeal mucosa	UBERON:0000355	90.56	gold quality
epithelium of nasopharynx	UBERON:0001951	90.49	gold quality
vena cava	UBERON:0004087	90.47	silver quality
gluteal muscle	UBERON:0002000	90.35	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	89.62	gold quality
pericardium	UBERON:0002407	89.51	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	89.46	gold quality
cartilage tissue	UBERON:0002418	89.34	gold quality
saphenous vein	UBERON:0007318	89.02	gold quality
tongue	UBERON:0001723	88.92	gold quality
deltoid	UBERON:0001476	88.89	gold quality
nipple	UBERON:0002030	88.67	gold quality
biceps brachii	UBERON:0001507	88.32	gold quality
superior surface of tongue	UBERON:0007371	88.19	gold quality
penis	UBERON:0000989	88.06	gold quality
dorsal root ganglion	UBERON:0000044	88.03	gold quality
tendon	UBERON:0000043	87.82	gold quality
skin of hip	UBERON:0001554	87.66	gold quality
urethra	UBERON:0000057	87.49	gold quality
pylorus	UBERON:0001166	87.26	gold quality
trachea	UBERON:0003126	87.13	gold quality
skeletal muscle tissue	UBERON:0001134	87.08	gold quality
renal medulla	UBERON:0000362	86.82	gold quality
quadriceps femoris	UBERON:0001377	86.80	gold quality
vastus lateralis	UBERON:0001379	86.62	gold quality
superior vestibular nucleus	UBERON:0007227	86.56	gold quality
cardia of stomach	UBERON:0001162	86.55	gold quality
synovial joint	UBERON:0002217	86.47	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.48

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

132 targeting BMS1, 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-513A-5P	100.00	69.77	2465
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-6873-3P	100.00	71.42	2626
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-5193	100.00	67.26	1744
HSA-MIR-8485	100.00	77.57	4731
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-548AN	99.97	70.91	2817
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-4666A-3P	99.96	71.71	3434
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753
HSA-MIR-2110	99.96	66.68	1930
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-548AB	99.95	71.31	3488
HSA-MIR-559	99.95	72.28	3609
HSA-MIR-9718	99.94	68.91	918
HSA-MIR-548AQ-5P	99.94	71.34	3426
HSA-MIR-548A-5P	99.94	71.27	3482
HSA-MIR-548AD-5P	99.94	71.23	3502
HSA-MIR-548AE-5P	99.94	71.23	3502
HSA-MIR-548AK	99.94	71.24	3488
HSA-MIR-548AM-5P	99.94	71.24	3488
HSA-MIR-548AP-5P	99.94	71.14	3489
HSA-MIR-548AR-5P	99.94	71.28	3515
HSA-MIR-548AS-5P	99.94	71.22	3482

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 99.5% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 4)

• Describes the distinct functions of yeast Bms1p and Tsr1p in ribosome biogenesis. (PMID:11565749)
• Analysis of KIAA0187 paralogs show that exons 14-23 were formed through satellite-associated pericentromeric-directed duplication, whereas paralogs of exons 1-9 evolved via chromosome-specific satellite-independent duplications. (PMID:11779832)
• The data provide a novel link between BMS1, the cell cycle, and skin morphogenesis. (PMID:23785305)
• We also observe evidence for an excess burden of rare, predicted loss-of-function variation in PXDNL and BMS1- two genes relevant to the broader laterality phenotype. These findings highlight potential new genes in the development of laterality defects, and suggest extensive locus heterogeneity and complex genetic models in this class of birth defects. (PMID:30622330)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	bms1	ENSDARG00000054154
mus_musculus	Bms1	ENSMUSG00000030138
rattus_norvegicus	Bms1	ENSRNOG00000006576
drosophila_melanogaster	CG7728	FBGN0036686
caenorhabditis_elegans		WBGENE00022021

Paralogs (1): TSR1 (ENSG00000167721)

Protein

Protein identifiers

Ribosome biogenesis protein BMS1 homolog — Q14692 (reviewed: Q14692)

Alternative names: Ribosome assembly protein BMS1 homolog

All UniProt accessions (1): Q14692

UniProt curated annotations — full annotation on UniProt →

Function. GTPase required for the synthesis of 40S ribosomal subunits and for processing of pre-ribosomal RNA (pre-rRNA) at sites A0, A1, and A2. Controls access of pre-rRNA intermediates to RCL1 during ribosome biogenesis by binding RCL1 in a GTP-dependent manner, and delivering it to pre-ribosomes. GTP-binding and/or GTP hydrolysis may induce conformational rearrangements within the BMS1-RCL1 complex allowing the interaction of RCL1 with its RNA substrate. Required for RCL1 import into the nucleus.

Subunit / interactions. Part of the small subunit (SSU) processome, composed of more than 70 proteins and the RNA chaperone small nucleolar RNA (snoRNA) U3. Interacts with RCL1.

Subcellular location. Nucleus. Nucleolus.

Disease relevance. Aplasia cutis congenita, non-syndromic (ACC) [MIM:107600] A disorder characterized by congenital absence of a portion of skin in a localized or widespread area of the body. The lesions are most commonly localized on the scalp, however aplasia cutis congenita can affect any part of the body. The disease is caused by variants affecting the gene represented in this entry.

Similarity. Belongs to the TRAFAC class translation factor GTPase superfamily. Bms1-like GTPase family. BMS1 subfamily.

RefSeq proteins (1): NP_055568* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR007034	BMS1_TSR1_C	Domain
IPR012948	AARP2CN	Domain
IPR027417	P-loop_NTPase	Homologous_superfamily
IPR030387	G_Bms1/Tsr1_dom	Domain
IPR037875	Bms1_N	Domain
IPR039761	Bms1/Tsr1	Family

Pfam: PF04950, PF08142

Catalyzed reactions (Rhea), 1 shown:

• GTP + H2O = GDP + phosphate + H(+) (RHEA:19669)

UniProt features (40 total): region of interest 11, compositionally biased region 8, cross-link 7, sequence variant 6, modified residue 5, chain 1, domain 1, binding site 1

Structure

Experimental structures (PDB)

3 structures.

PDB	Method	Resolution (Å)
7MQA	ELECTRON MICROSCOPY	2.7
7MQ8	ELECTRON MICROSCOPY	3.6
7MQ9	ELECTRON MICROSCOPY	3.87

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q14692-F1	72.04	0.38

Functional residue map

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

Ligand- & substrate-binding residues (1): 89–96

Post-translational modifications (12): 188, 552, 625, 639, 708, 43, 399, 415, 646, 810, 810, 1206

Function

Pathways and Gene Ontology

Reactome pathways

5 pathways

ID	Pathway
R-HSA-6790901	rRNA modification in the nucleus and cytosol
R-HSA-6791226	Major pathway of rRNA processing in the nucleolus and cytosol
R-HSA-72312	rRNA processing
R-HSA-8868773	rRNA processing in the nucleus and cytosol
R-HSA-8953854	Metabolism of RNA

MSigDB gene sets: 221 (showing top): GSE45365_CD8A_DC_VS_CD11B_DC_IFNAR_KO_MCMV_INFECTION_UP, GOBP_RIBOSOME_BIOGENESIS, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP, GOBP_MATURATION_OF_SSU_RRNA, LINDGREN_BLADDER_CANCER_CLUSTER_3_DN, MORF_HDAC2, SHEPARD_BMYB_MORPHOLINO_DN, MONNIER_POSTRADIATION_TUMOR_ESCAPE_UP, GGAANCGGAANY_UNKNOWN, GOBP_RIBOSOMAL_SMALL_SUBUNIT_BIOGENESIS, MORF_FANCG, GOBP_MATURATION_OF_SSU_RRNA_FROM_TRICISTRONIC_RRNA_TRANSCRIPT_SSU_RRNA_5_8S_RRNA_LSU_RRNA, MORF_PRKDC, MORF_RAP1A, MORF_AATF

GO Biological Process (4): maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000462), endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000479), ribosomal small subunit biogenesis (GO:0042274), ribosome biogenesis (GO:0042254)

GO Molecular Function (8): RNA binding (GO:0003723), GTPase activity (GO:0003924), ATP binding (GO:0005524), GTP binding (GO:0005525), U3 snoRNA binding (GO:0034511), nucleotide binding (GO:0000166), protein binding (GO:0005515), hydrolase activity (GO:0016787)

GO Cellular Component (5): nucleoplasm (GO:0005654), chromosome (GO:0005694), nucleolus (GO:0005730), small-subunit processome (GO:0032040), nucleus (GO:0005634)

Reactome top-level categories

Rollup of top-3 pathways:

Category	Pathways
rRNA processing in the nucleus and cytosol	2
Metabolism of RNA	1
rRNA processing	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
ribonucleoprotein complex biogenesis	2
purine ribonucleoside triphosphate binding	2
nuclear lumen	2
intracellular membraneless organelle	2
maturation of SSU-rRNA	1
rRNA processing	1
ribosome biogenesis	1
nucleic acid binding	1
ribonucleoside triphosphate phosphatase activity	1
adenyl ribonucleotide binding	1
guanyl ribonucleotide binding	1
snoRNA binding	1
nucleoside phosphate binding	1
heterocyclic compound binding	1
binding	1
catalytic activity	1
cellular anatomical structure	1
nucleolus	1
preribosome	1
t-UTP complex	1
nuclear protein-containing complex	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

3104 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
BMS1	RCL1	Q9Y2P8	999
BMS1	RTCA	O00442	853
BMS1	NOP14	P78316	811
BMS1	NOP56	O00567	803
BMS1	BYSL	Q13895	801
BMS1	UTP15	Q8TED0	778
BMS1	UTP4	Q969X6	765
BMS1	RIOK2	Q9BVS4	764
BMS1	NAT10	Q9H0A0	763
BMS1	UTP14A	Q9BVJ6	756
BMS1	NOP58	Q9Y2X3	749
BMS1	NOB1	Q9ULX3	747
BMS1	PNO1	Q9NRX1	738
BMS1	DDX52	Q9Y2R4	732
BMS1	RRP12	Q5JTH9	722

IntAct

203 interactions, top by confidence:

A	B	Type	Score
LARP7	CCNT1	psi-mi:“MI:0914”(association)	0.850
BMS1	RCL1	psi-mi:“MI:0915”(physical association)	0.690
RCL1	BMS1	psi-mi:“MI:0914”(association)	0.690
RCL1	BMS1	psi-mi:“MI:0915”(physical association)	0.690
LIN28A	IGF2BP3	psi-mi:“MI:0914”(association)	0.640
NPM1	MPHOSPH10	psi-mi:“MI:0914”(association)	0.610
ZNF2	MPHOSPH10	psi-mi:“MI:0914”(association)	0.530
MACROH2A2	PPM1G	psi-mi:“MI:0914”(association)	0.530
RPL18A	RRP8	psi-mi:“MI:0914”(association)	0.530
ZBTB48	ZBTB24	psi-mi:“MI:0914”(association)	0.530
PDGFB	DKC1	psi-mi:“MI:0914”(association)	0.530
RPSA	DKC1	psi-mi:“MI:0914”(association)	0.530
N	NOP56	psi-mi:“MI:0914”(association)	0.530
N	RBM47	psi-mi:“MI:0914”(association)	0.530
RPS3	ZNF316	psi-mi:“MI:0914”(association)	0.530
MAGEB2	POLRMT	psi-mi:“MI:0914”(association)	0.530
H2BC26	PPM1G	psi-mi:“MI:0914”(association)	0.530
RPSA	RPS17	psi-mi:“MI:0914”(association)	0.530
MAGEB2	GTPBP10	psi-mi:“MI:0914”(association)	0.530
RPS2	MPHOSPH10	psi-mi:“MI:0914”(association)	0.530
KRR1	MPHOSPH10	psi-mi:“MI:0914”(association)	0.530
ABT1	ZNF316	psi-mi:“MI:0914”(association)	0.530
RBM19	KRR1	psi-mi:“MI:0914”(association)	0.530
FOXM1	PES1	psi-mi:“MI:0914”(association)	0.500
DDX21	MED19	psi-mi:“MI:2364”(proximity)	0.480
BMS1	CSNK2A1	psi-mi:“MI:0217”(phosphorylation reaction)	0.440

BioGRID (280): BMS1 (Affinity Capture-RNA), BMS1 (Affinity Capture-RNA), BMS1 (Affinity Capture-MS), BMS1 (Affinity Capture-MS), BMS1 (Affinity Capture-MS), RRS1 (Co-fractionation), BMS1 (Affinity Capture-MS), BMS1 (Affinity Capture-MS), BMS1 (Affinity Capture-MS), BMS1 (Affinity Capture-MS), BMS1 (Proximity Label-MS), BMS1 (Affinity Capture-MS), BMS1 (Affinity Capture-MS), BMS1 (Affinity Capture-MS), BMS1 (Affinity Capture-MS)

ESM2 similar proteins: A1ZA92, A3KN83, A8E7C5, A8PJX4, A8WP66, B0W730, B3MJV4, B4GH42, B4HWV2, B4JE52, B4MV81, B4Q9T2, B5E0H4, O13956, O59800, O62301, O74788, O89042, O94653, P09884, P13382, P28040, P33609, P39730, P53893, Q07381, Q08965, Q09475, Q10251, Q14692, Q17G65, Q17LZ2, Q19329, Q5F371, Q61WR2, Q689Z5, Q75DC5, Q7PTC5, Q851S7, Q8CDA1

Diamond homologs: O94653, Q08965, Q14692, Q5VTM2, Q5XGY1, A1L520, A5PK26, A6NIR3, D3YUJ3, O74345, O75689, O80925, O82171, O94601, O97902, P35197, P38682, P40529, Q04412, Q09531, Q0WQQ1, Q10165, Q14161, Q15027, Q15057, Q17R07, Q1AAU6, Q1ZXH8, Q28CM8, Q3MID3, Q3UHD9, Q4KLN7, Q4R4C9, Q4R871, Q5EA00, Q5F413, Q5FVC7, Q5R787, Q5RAT7, Q5T2Q4

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 191 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
Formation of Senescence-Associated Heterochromatin Foci (SAHF)	6	32.5×	2e-07
Eukaryotic Translation Initiation	12	29.9×	6e-14
Cap-dependent Translation Initiation	12	29.9×	6e-14
SARS-CoV-1 modulates host translation machinery	12	29.9×	6e-14
Peptide chain elongation	29	29.7×	1e-33
Viral mRNA Translation	29	29.7×	1e-33
PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA	29	29.4×	1e-33
Selenocysteine synthesis	29	28.1×	3e-33

GO biological processes:

GO term	Partners	Fold	FDR
negative regulation of DNA recombination	6	40.1×	7e-07
cytoplasmic translation	30	33.1×	3e-35
chromosome condensation	6	30.1×	4e-06
ribosomal small subunit biogenesis	15	20.3×	2e-13
ribosomal large subunit biogenesis	7	18.5×	9e-06
translation	29	17.7×	1e-25
rRNA processing	17	14.3×	6e-13
negative regulation of translation	9	10.5×	2e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	181
Likely benign	37
Benign	20

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
155924	NM_014753.4(BMS1):c.2789G>A (p.Arg930His)	Pathogenic

SpliceAI

3167 predictions. Top by Δscore:

Variant	Effect	Δscore
10:42784357:TGTA:T	acceptor_loss	1.0000
10:42784358:GTA:G	acceptor_loss	1.0000
10:42784359:TA:T	acceptor_loss	1.0000
10:42784361:GGTT:G	acceptor_gain	1.0000
10:42784361:GGTTA:G	acceptor_gain	1.0000
10:42784571:G:GA	donor_loss	1.0000
10:42784571:G:GG	donor_gain	1.0000
10:42785473:A:AG	acceptor_gain	1.0000
10:42785473:AAT:A	acceptor_gain	1.0000
10:42785474:A:AG	acceptor_gain	1.0000
10:42785474:AT:A	acceptor_gain	1.0000
10:42785475:T:G	acceptor_gain	1.0000
10:42785475:T:TA	acceptor_gain	1.0000
10:42785478:ATAG:A	acceptor_gain	1.0000
10:42785479:T:G	acceptor_gain	1.0000
10:42785480:A:AG	acceptor_gain	1.0000
10:42785480:AG:A	acceptor_gain	1.0000
10:42785481:G:GA	acceptor_gain	1.0000
10:42785481:GG:G	acceptor_gain	1.0000
10:42785481:GGA:G	acceptor_gain	1.0000
10:42785481:GGAC:G	acceptor_gain	1.0000
10:42787162:TTATA:T	acceptor_loss	1.0000
10:42787163:TATAG:T	acceptor_loss	1.0000
10:42787165:TA:T	acceptor_loss	1.0000
10:42787166:A:AG	acceptor_gain	1.0000
10:42787166:AGGT:A	acceptor_loss	1.0000
10:42787167:G:GG	acceptor_gain	1.0000
10:42787245:CTGG:C	donor_loss	1.0000
10:42787246:TGGTA:T	donor_loss	1.0000
10:42790500:G:GT	donor_gain	1.0000

AlphaMissense

8569 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
10:42790472:G:C	K199N	1.000
10:42790472:G:T	K199N	1.000
10:42791637:T:C	L216P	1.000
10:42785570:G:A	G89R	0.999
10:42785570:G:C	G89R	0.999
10:42785610:T:C	L102P	0.999
10:42787246:T:C	L149P	0.999
10:42790378:T:C	L168P	0.999
10:42790416:G:A	G181R	0.999
10:42790416:G:C	G181R	0.999
10:42790417:G:A	G181E	0.999
10:42790423:T:A	L183H	0.999
10:42790423:T:C	L183P	0.999
10:42790432:T:A	L186H	0.999
10:42790484:A:C	K203N	0.999
10:42790484:A:T	K203N	0.999
10:42790492:T:C	F206S	0.999
10:42790494:T:A	W207R	0.999
10:42790494:T:C	W207R	0.999
10:42790496:G:C	W207C	0.999
10:42790496:G:T	W207C	0.999
10:42791631:C:A	A214D	0.999
10:42791637:T:A	L216Q	0.999
10:42791694:T:C	L235P	0.999
10:42791700:G:C	R237P	0.999
10:42791702:T:C	F238L	0.999
10:42791704:T:A	F238L	0.999
10:42791704:T:G	F238L	0.999
10:42820580:T:A	W948R	0.999
10:42820580:T:C	W948R	0.999

dbSNP variants (sampled 300 via entrez): RS1000004809 (10:42826007 T>A,C), RS1000019535 (10:42803473 A>G,T), RS1000134116 (10:42807039 G>C), RS1000241719 (10:42800948 C>T), RS1000342909 (10:42800881 G>T), RS1000348818 (10:42807207 C>T), RS1000401353 (10:42807520 G>A), RS1000428193 (10:42812633 G>C), RS1000442348 (10:42794207 C>T), RS1000455833 (10:42800669 G>A,T), RS1000826873 (10:42795721 G>A), RS1000860218 (10:42802338 G>A,T), RS1000940128 (10:42835227 T>C,G), RS1000996807 (10:42784203 A>G), RS1001117282 (10:42818452 A>G)

Disease associations

OMIM: gene MIM:611448 | disease phenotypes: MIM:107600

GenCC curated gene-disease

Disease	Classification	Inheritance
aplasia cutis congenita	Strong	Autosomal dominant

Mondo (1): aplasia cutis congenita (MONDO:0007145)

Orphanet (1): Aplasia cutis congenita (Orphanet:1114)

HPO phenotypes

14 total (14 of 14 shown, HPO-id order):

HPO	Term
HP:0000006	Autosomal dominant inheritance
HP:0001057	Aplasia cutis congenita
HP:0001362	Calvarial skull defect
HP:0001770	Toe syndactyly
HP:0003010	Prolonged bleeding time
HP:0004348	Abnormality of bone mineral density
HP:0004471	Aplasia cutis congenita over the scalp vertex
HP:0006101	Finger syndactyly
HP:0007383	Congenital localized absence of skin
HP:0010301	Spinal dysraphism
HP:0010628	Facial palsy
HP:0010783	Erythema
HP:0200042	Skin ulcer
HP:5200061	Tactile hypersensitivity

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST001116_10	Progressive supranuclear palsy	3.000000e-07
GCST008162_105	Hip circumference	7.000000e-06

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
bisphenol A	decreases expression, affects cotreatment	2
sodium arsenite	decreases expression, increases abundance, increases expression	2
bisphenol S	affects expression, affects cotreatment, decreases expression	2
aristolochic acid I	decreases expression	1
FR900359	affects phosphorylation	1
TAK-243	decreases sumoylation	1
triphenyl phosphate	affects expression	1
deoxynivalenol	increases expression	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
coumarin	increases phosphorylation	1
CGP 52608	affects binding, increases reaction	1
Temozolomide	increases expression	1
Arsenic	increases abundance, increases expression	1
Benzo(a)pyrene	increases expression	1
Caffeine	affects phosphorylation	1
Dexamethasone	affects cotreatment, decreases expression	1
Diazinon	increases methylation	1
Enzyme Inhibitors	decreases activity, increases O-linked glycosylation	1
Estradiol	increases expression	1
Hydrogen Peroxide	affects expression	1
Indomethacin	affects cotreatment, decreases expression	1
Ivermectin	decreases expression	1
Ribonucleotides	affects binding	1
Tetrachlorodibenzodioxin	affects expression	1
Tretinoin	decreases expression	1
Valproic Acid	affects expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, decreases expression	1
Aflatoxin B1	affects cotreatment, decreases expression	1
Cadmium Chloride	decreases expression	1
beta-Naphthoflavone	affects cotreatment, decreases expression	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT01678105	PHASE2	COMPLETED	A Phase II Study of Dovitinib in Recurrent and/or Metastatic Adenoid Cystic Carcinoma of the Salivary Glands
NCT06066333	PHASE2	RECRUITING	Study of Radiotherapy and Pembrolizumab in People With Adrenocortical Carcinoma
NCT01898715	PHASE1	COMPLETED	Phase 1 Study of ATR-101 in Subjects With Advanced Adrenocortical Carcinoma
NCT01262235	PHASE1/PHASE2	COMPLETED	A Dose Finding Study of TKM-080301 Infusion in Neuroendocrine Tumors (NET) and Adrenocortical Carcinoma (ACC) Patients
NCT00170326	Not specified	COMPLETED	Progressive Ventricular Dysfunction Prevention in Pacemaker Patients
NCT01117792	Not specified	COMPLETED	Subcutaneous Implantable Defibrillator (S-ICD) System - CE Clinical Investigation
NCT01630421	Not specified	RECRUITING	Genetic and Functional Analysis of Aplasia Cutis Congenital (ACC)