ADAMTSL1

Summary

ADAMTSL1 (ADAMTS like 1, HGNC:14632) is a protein-coding gene on chromosome 9p22.2-p22.1, encoding ADAMTS-like protein 1 (Q8N6G6).

This gene encodes a secreted protein and member of the ADAMTS (a disintegrin and metalloproteinase with thrombospondin motif) family. This protein lacks the metalloproteinase and disintegrin-like domains, which are typical of the ADAMTS family, but contains other ADAMTS domains, including the thrombospondin type 1 motif. This protein may have important functions in the extracellular matrix. Alternative splicing results in multiple transcript variants encoding distinct proteins.

Source: NCBI Gene 92949 — RefSeq curated summary.

At a glance

• GWAS associations: 30
• Clinical variants (ClinVar): 417 total — 8 pathogenic
• Phenotypes (HPO): 27
• MANE Select transcript: NM_001040272

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:14632
Approved symbol	ADAMTSL1
Name	ADAMTS like 1
Location	9p22.2-p22.1
Locus type	gene with protein product
Status	Approved
Aliases	ADAMTSR1, FLJ35283
Ensembl gene	ENSG00000178031
Ensembl biotype	protein_coding
OMIM	609198
Entrez	92949

Gene structure

Transcript identifiers

Ensembl transcripts: 16 — 10 protein_coding, 3 retained_intron, 2 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000276935, ENST00000327883, ENST00000380538, ENST00000380545, ENST00000380548, ENST00000380559, ENST00000380566, ENST00000380570, ENST00000388710, ENST00000431052, ENST00000489062, ENST00000496521, ENST00000542621, ENST00000546040, ENST00000680146, ENST00000872893

RefSeq mRNA: 2 — MANE Select: NM_001040272 NM_001040272, NM_052866

CCDS: CCDS47954, CCDS6485

Canonical transcript exons

ENST00000380548 — 29 exons

Exon	Start	End
ENSE00000982244	18657639	18657750
ENSE00000982246	18675857	18675907
ENSE00001089601	18706747	18707048
ENSE00001295594	18639254	18639411
ENSE00001303038	18533247	18533292
ENSE00001309461	18622243	18622369
ENSE00001313382	18504829	18504956
ENSE00001315290	18635943	18636017
ENSE00001330201	18574030	18574266
ENSE00001367200	18684716	18684800
ENSE00001388413	18474153	18474295
ENSE00001729064	18908442	18910950
ENSE00003464322	18770602	18770781
ENSE00003490484	18892389	18892596
ENSE00003509522	18817109	18817237
ENSE00003519309	18906692	18906912
ENSE00003525275	18829843	18829977
ENSE00003554442	18776781	18777906
ENSE00003587484	18905782	18905891
ENSE00003598950	18775743	18775896
ENSE00003606968	18887831	18888043
ENSE00003608272	18826284	18826463
ENSE00003609308	18795397	18795524
ENSE00003609855	18889568	18889748
ENSE00003614019	18681812	18681959
ENSE00003633997	18721536	18721665
ENSE00003644436	18753298	18753508
ENSE00003662712	18680312	18680516
ENSE00003676296	18661935	18662073

Expression profiles

Bgee: expression breadth ubiquitous, 182 present calls, max score 88.96.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 19.0191 / max 775.4613, expressed in 936 samples.

FANTOM5 promoters (8 alternative TSS)

Promoter ID	TPM avg	Samples expressed
96226	12.4091	817
96227	5.6313	674
96228	0.5208	260
96221	0.2275	82
96222	0.1383	43
96219	0.0540	27
96218	0.0212	11
96220	0.0169	10

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
lower esophagus muscularis layer	UBERON:0035833	88.96	gold quality
lower esophagus	UBERON:0013473	88.85	gold quality
sural nerve	UBERON:0015488	87.46	gold quality
descending thoracic aorta	UBERON:0002345	86.92	gold quality
thoracic aorta	UBERON:0001515	86.06	gold quality
ascending aorta	UBERON:0001496	85.99	gold quality
body of uterus	UBERON:0009853	85.94	gold quality
smooth muscle tissue	UBERON:0001135	84.14	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	84.07	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	82.69	gold quality
oviduct epithelium	UBERON:0004804	82.52	gold quality
cortical plate	UBERON:0005343	82.21	gold quality
kidney epithelium	UBERON:0004819	81.03	silver quality
left uterine tube	UBERON:0001303	80.74	gold quality
tibial nerve	UBERON:0001323	80.41	gold quality
esophagus	UBERON:0001043	79.44	gold quality
left adrenal gland cortex	UBERON:0035825	79.36	gold quality
myometrium	UBERON:0001296	78.68	gold quality
left adrenal gland	UBERON:0001234	78.61	gold quality
right adrenal gland cortex	UBERON:0035827	78.56	gold quality
aorta	UBERON:0000947	78.46	gold quality
colonic epithelium	UBERON:0000397	78.43	gold quality
mucosa of stomach	UBERON:0001199	78.29	gold quality
right adrenal gland	UBERON:0001233	78.17	gold quality
adrenal cortex	UBERON:0001235	78.15	gold quality
mucosa of transverse colon	UBERON:0004991	77.91	gold quality
endocervix	UBERON:0000458	77.88	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	77.84	gold quality
adrenal gland	UBERON:0002369	77.55	gold quality
fallopian tube	UBERON:0003889	77.00	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-CURD-119	yes	41.42
E-ANND-3	yes	12.44
E-GEOD-124858	no	163.10

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): TP53

miRNA regulators (miRDB)

146 targeting ADAMTSL1, 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-5692A	100.00	74.40	6850
HSA-MIR-6867-5P	100.00	82.21	3464
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-513A-5P	100.00	69.77	2465
HSA-MIR-3064-3P	100.00	70.09	1254
HSA-MIR-126-5P	100.00	72.71	3180
HSA-MIR-4481	100.00	66.42	1669
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-4455	100.00	65.48	1587
HSA-MIR-3120-5P	100.00	65.56	965
HSA-MIR-4682	100.00	68.89	1258
HSA-MIR-6873-3P	100.00	71.42	2626
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-3185	99.99	68.12	1959
HSA-MIR-513B-5P	99.99	69.96	2150
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-3662	99.99	73.82	5684
HSA-MIR-32-5P	99.98	75.21	1964
HSA-MIR-92A-3P	99.98	75.21	1960
HSA-MIR-92B-3P	99.98	75.25	1955
HSA-MIR-25-3P	99.98	74.60	1817
HSA-MIR-363-3P	99.98	74.72	1821
HSA-MIR-367-3P	99.98	74.83	1819
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-LET-7F-2-3P	99.98	70.98	2588

Literature-anchored findings (GeneRIF, showing 6)

• Punctin, a novel ADAMTS-like molecule, ADAMTSL-1, in extracellular matrix (PMID:11805097)
• data define a critical role for N-glycosylation and O-fucosylation in the biosynthesis of punctin-1 (PMID:17395588)
• thrombospondin type-1 repeats from punctin-1 carries C-mannosylation in close proximity to O-linked fucose (PMID:19671700)
• These data imply a multisystem role for ADAMTSL1 and present the first disease-associated variant affecting a C-mannosylation motif. (PMID:28722276)
• ADAMTSL1 are associated with breast cancer prognosis and may involve an interaction with AREG expression. (PMID:29158497)
• This explains why the patients with ADAMTSL1 mutations had abnormal mandibles but normal long bones. This is the first report that mutations in ADAMTSL1 are responsible for the pathogenesis of mandibular prognathism. (PMID:30714143)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Adamtsl1	ENSMUSG00000066113
rattus_norvegicus	Adamtsl1	ENSRNOG00000006956

Paralogs (25): ADAMTS6 (ENSG00000049192), ADAMTS2 (ENSG00000087116), PAPLN (ENSG00000100767), ADAMTS8 (ENSG00000134917), ADAMTS7 (ENSG00000136378), ADAMTS14 (ENSG00000138316), ADAMTS17 (ENSG00000140470), ADAMTS18 (ENSG00000140873), ADAMTS10 (ENSG00000142303), ADAMTSL4 (ENSG00000143382), ADAMTS16 (ENSG00000145536), ADAMTS19 (ENSG00000145808), ADAMTS12 (ENSG00000151388), ADAMTS1 (ENSG00000154734), ADAMTS5 (ENSG00000154736), ADAMTS3 (ENSG00000156140), ADAMTSL3 (ENSG00000156218), ADAMTS4 (ENSG00000158859), ADAMTS13 (ENSG00000160323), ADAMTS9 (ENSG00000163638), ADAMTS15 (ENSG00000166106), ADAMTS20 (ENSG00000173157), ADAMTSL5 (ENSG00000185761), THSD4 (ENSG00000187720), ADAMTSL2 (ENSG00000197859)

Protein

Protein identifiers

ADAMTS-like protein 1 — Q8N6G6 (reviewed: Q8N6G6)

Alternative names: Punctin-1

All UniProt accessions (6): A0A7P0T9B9, A2A343, A6NIB9, F8WEP3, H7BYE3, Q8N6G6

UniProt curated annotations — full annotation on UniProt →

Subunit / interactions. Monomer.

Subcellular location. Secreted. Extracellular space. Extracellular matrix.

Tissue specificity. Expressed primarily in adult skeletal muscle.

Post-translational modifications. C-, N- and O-glycosylated. O-fucosylated by POFUT2 on a serine or a threonine residue found within the consensus sequence C1-X(2)-(S/T)-C2-G of the TSP type-1 repeat domains where C1 and C2 are the first and second cysteine residue of the repeat, respectively. Fucosylated repeats can then be further glycosylated by the addition of a beta-1,3-glucose residue by the glucosyltransferase, B3GALTL. Fucosylation mediates the efficient secretion of ADAMTSL1. Can also be C-glycosylated with one or two mannose molecules on tryptophan residues within the consensus sequence W-X-X-W of the TPRs, and N-glycosylated. These other glycosylations can also facilitate secretion. Disulfide bonds are present.

Miscellaneous. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

Isoforms (6)

UniProt ID	Names	Canonical?
Q8N6G6-3	3	yes
Q8N6G6-1	1
Q8N6G6-2	2
Q8N6G6-4	4
Q8N6G6-5	5
Q8N6G6-6	6

RefSeq proteins (2): NP_001035362, NP_443098 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000884	TSP1_rpt	Repeat
IPR003598	Ig_sub2	Domain
IPR003599	Ig_sub	Domain
IPR007110	Ig-like_dom	Domain
IPR010294	ADAMTS_spacer1	Domain
IPR010909	PLAC	Domain
IPR013098	Ig_I-set	Domain
IPR013273	ADAMTS/ADAMTS-like	Family
IPR013783	Ig-like_fold	Homologous_superfamily
IPR036179	Ig-like_dom_sf	Homologous_superfamily
IPR036383	TSP1_rpt_sf	Homologous_superfamily
IPR045371	ADAMTS_CR_3	Domain
IPR050439	ADAMTS_ADAMTS-like	Family
IPR056272	ADAMTSL1_dom	Domain

Pfam: PF00090, PF05986, PF07679, PF08686, PF13927, PF19030, PF19236, PF24484

UniProt features (68 total): disulfide bond 16, domain 14, mutagenesis site 12, splice variant 10, glycosylation site 7, sequence conflict 3, signal peptide 1, chain 1, region of interest 1, compositionally biased region 1, site 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N6G6-F1	71.26	0.07

Functional residue map

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

Catalytic / active sites (1): 36 (not glycosylated)

Disulfide bonds (16): 45–76, 49–81, 60–66, 534–578, 538–583, 549–567, 678–723, 682–728, 693–712, 800–844, 804–849, 815–832, 899–947, 1202–1250, 1308–1353, 1418–1469

Glycosylation sites (7): 39, 42, 48, 251, 312, 391, 451

Mutagenesis-validated functional residues (12):

Position	Phenotype
36	small reduction in secretion of adamtsl1.
39	significant reduction in secretion of adamtsl1.
39	abolishes secretion of adamtsl1.
42	modest reduction in secretion of adamtsl1.
42	abolishes secretion of adamtsl1.
251	abolishes n-glycosylation. reduces secretion of adamtsl1.
312	small increase in secretion of adamtsl1. about 40% increase in secretion of adamtsl1; when associated with a-391. dramat
385	significant reduction in secretion of adamtsl1.
385	no effect on secretion of adamtsl1.
391	small increase in secretion of adamtsl1. about 40% increase in secretion of adamtsl1; when associated with a-312. dramat
445	modest reduction in secretion of adamtsl1.
451	small increase in secretion of adamtsl1. dramatic increase in secretion of adamtsl1; when associated with a-312 and a-39

Function

Pathways and Gene Ontology

Reactome pathways

9 pathways

ID	Pathway
R-HSA-5083635	Defective B3GALTL causes PpS
R-HSA-5173214	O-glycosylation of TSR domain-containing proteins
R-HSA-1643685	Disease
R-HSA-3781865	Diseases of glycosylation
R-HSA-3906995	Diseases associated with O-glycosylation of proteins
R-HSA-392499	Metabolism of proteins
R-HSA-5173105	O-linked glycosylation
R-HSA-5668914	Diseases of metabolism
R-HSA-597592	Post-translational protein modification

MSigDB gene sets: 225 (showing top): PAX4_01, AREB6_01, TAKADA_GASTRIC_CANCER_COPY_NUMBER_DN, SRF_Q5_01, CATRRAGC_UNKNOWN, NF1_Q6_01, KMCATNNWGGA_UNKNOWN, WTGAAAT_UNKNOWN, TGANTCA_AP1_C, GATA1_04, GATA1_03, AACTTT_UNKNOWN, RYTTCCTG_ETS2_B, FOXJ2_02, PIT1_Q6

GO Biological Process (1): extracellular matrix organization (GO:0030198)

GO Molecular Function (1): hydrolase activity (GO:0016787)

GO Cellular Component (2): endoplasmic reticulum lumen (GO:0005788), extracellular region (GO:0005576)

Reactome top-level categories

Rollup of top-7 pathways:

Category	Pathways
Diseases associated with O-glycosylation of proteins	1
O-linked glycosylation	1
Diseases of metabolism	1
Diseases of glycosylation	1
Post-translational protein modification	1
Disease	1
Metabolism of proteins	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
extracellular structure organization	1
external encapsulating structure organization	1
catalytic activity	1
endoplasmic reticulum	1
intracellular organelle lumen	1
cellular anatomical structure	1

Protein interactions and networks

STRING

832 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ADAMTSL1	MTAP	Q13126	676
ADAMTSL1	TYRP1	P17643	549
ADAMTSL1	POFUT2	Q9Y2G5	547
ADAMTSL1	HSD17B8	Q92506	470
ADAMTSL1	B3GLCT	Q6Y288	454
ADAMTSL1	TSR1	Q2NL82	436
ADAMTSL1	CHPT1	Q8WUD6	429
ADAMTSL1	DPY19L1	Q2PZI1	427
ADAMTSL1	TSR3	Q9UJK0	413
ADAMTSL1	PDE8B	O95263	413
ADAMTSL1	DPY19L3	Q6ZPD9	406
ADAMTSL1	AGBL4	Q5VU57	401
ADAMTSL1	SLC7A5	Q01650	378
ADAMTSL1	CCDC171	Q6TFL3	350
ADAMTSL1	ADAM28	Q9UKQ2	347

IntAct

3 interactions, top by confidence:

A	B	Type	Score
LPAR1	TMEM223	psi-mi:“MI:0914”(association)	0.530
ADAMTSL1	GRN	psi-mi:“MI:0914”(association)	0.350

BioGRID (20): B3GALTL (Affinity Capture-MS), FHL2 (Affinity Capture-MS), RSPRY1 (Affinity Capture-MS), C2orf44 (Affinity Capture-MS), ACOX1 (Affinity Capture-MS), FBN2 (Affinity Capture-MS), GRN (Affinity Capture-MS), ADAMTSL1 (Affinity Capture-MS), B3GALTL (Affinity Capture-MS), FBN2 (Affinity Capture-MS), RSPRY1 (Affinity Capture-MS), FHL2 (Affinity Capture-MS), C2orf44 (Affinity Capture-MS), GRN (Affinity Capture-MS), ACOX1 (Affinity Capture-MS)

ESM2 similar proteins: A7MBS7, D3YXF5, F1LW30, O89103, P10643, P11680, P27918, P35446, P82987, P90884, Q29RQ1, Q2I0M5, Q2MKA7, Q3UPR9, Q3UTY6, Q4R7Z5, Q5M7L6, Q5RAD0, Q5RBP1, Q5RBP8, Q5UE90, Q64181, Q66PY1, Q69ZU6, Q6NZL8, Q6P4U0, Q6UXX9, Q6ZMP0, Q7T3Q2, Q7TSK7, Q80YN4, Q86TH1, Q8BFU0, Q8BJ73, Q8BLI0, Q8IUX8, Q8IWY4, Q8IX30, Q8N6G6, Q8VCC9

Diamond homologs: B3EWY9, B3EWZ3, B3EWZ8, C0HL12, C5IAW9, D3YXG0, D3ZTD8, E9Q6D8, F1LW30, O08721, O08722, O08747, O15072, O60242, O75173, O76840, O95185, O95428, O95450, P07357, P07996, P11680, P13671, P17347, P35440, P35441, P35442, P35448, P57110, P58397, P58459, P59384, P59511, P61134, P61135, P79331, P82987, P83255, P85314, P97857

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	8
Likely pathogenic	0
Uncertain significance	335
Likely benign	33
Benign	7

Top pathogenic / likely-pathogenic (8)

Variant ID	HGVS	Classification
144343	GRCh38/hg38 9p24.3-22.2(chr9:204193-18073359)x1	Pathogenic
146356	GRCh38/hg38 9p24.3-22.1(chr9:220253-18708805)x1	Pathogenic
146394	GRCh38/hg38 9p24.3-22.1(chr9:204104-18882281)x1	Pathogenic
147568	GRCh38/hg38 9p22.2-22.1(chr9:17502887-18681091)x3	Pathogenic
1703681	GRCh37/hg19 9p24.1-22.1(chr9:4992582-19322101)	Pathogenic
3063070	GRCh37/hg19 9p24.3-22.1(chr9:203861-19302836)x1	Pathogenic
563685	GRCh37/hg19 9p24.3-q13(chr9:203861-68262804)x3,4	Pathogenic
59064	GRCh38/hg38 9p24.3-22.2(chr9:220253-18073359)x1	Pathogenic

SpliceAI

4754 predictions. Top by Δscore:

Variant	Effect	Δscore
9:18504827:A:AG	acceptor_gain	1.0000
9:18504828:G:GG	acceptor_gain	1.0000
9:18504828:GA:G	acceptor_gain	1.0000
9:18504953:GCAA:G	donor_gain	1.0000
9:18504957:G:GG	donor_gain	1.0000
9:18533237:T:TA	acceptor_gain	1.0000
9:18533240:A:AG	acceptor_gain	1.0000
9:18533241:A:G	acceptor_gain	1.0000
9:18533246:G:T	acceptor_loss	1.0000
9:18533246:GGA:G	acceptor_gain	1.0000
9:18533290:GTG:G	donor_gain	1.0000
9:18533291:TG:T	donor_gain	1.0000
9:18533291:TGG:T	donor_loss	1.0000
9:18533292:GG:G	donor_gain	1.0000
9:18533293:G:GG	donor_gain	1.0000
9:18533294:TAAG:T	donor_loss	1.0000
9:18574025:TCCA:T	acceptor_loss	1.0000
9:18574027:CAG:C	acceptor_loss	1.0000
9:18574028:A:AG	acceptor_gain	1.0000
9:18574028:AG:A	acceptor_gain	1.0000
9:18574029:G:GG	acceptor_gain	1.0000
9:18574029:GG:G	acceptor_gain	1.0000
9:18574029:GGA:G	acceptor_gain	1.0000
9:18574029:GGAC:G	acceptor_gain	1.0000
9:18574029:GGACT:G	acceptor_gain	1.0000
9:18574262:GCCAA:G	donor_gain	1.0000
9:18574267:G:GG	donor_gain	1.0000
9:18622370:G:GG	donor_gain	1.0000
9:18635937:CTCTA:C	acceptor_loss	1.0000
9:18635938:TCTA:T	acceptor_loss	1.0000

AlphaMissense

11447 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
9:18504882:G:C	W39C	1.000
9:18504882:G:T	W39C	1.000
9:18574055:T:G	F88C	1.000
9:18574069:T:A	C93S	1.000
9:18574070:G:C	C93S	1.000
9:18574116:G:C	W108C	1.000
9:18574116:G:T	W108C	1.000
9:18657705:T:A	W301R	1.000
9:18657705:T:C	W301R	1.000
9:18657707:G:C	W301C	1.000
9:18657707:G:T	W301C	1.000
9:18680510:G:C	W445C	1.000
9:18680510:G:T	W445C	1.000
9:18777871:G:C	W1214C	1.000
9:18777871:G:T	W1214C	1.000
9:18892407:G:C	W1554C	1.000
9:18892407:G:T	W1554C	1.000
9:18504873:G:C	W36C	0.999
9:18504873:G:T	W36C	0.999
9:18504891:G:C	W42C	0.999
9:18504891:G:T	W42C	0.999
9:18533281:T:C	C76R	0.999
9:18574069:T:C	C93R	0.999
9:18574071:C:G	C93W	0.999
9:18574114:T:A	W108R	0.999
9:18574114:T:C	W108R	0.999
9:18574159:T:A	C123S	0.999
9:18574159:T:C	C123R	0.999
9:18574160:G:C	C123S	0.999
9:18574161:C:G	C123W	0.999

dbSNP variants (sampled 300 via entrez): RS1000004208 (9:18468950 A>C), RS1000005319 (9:18512199 C>G,T), RS1000012207 (9:17915428 T>C), RS1000013664 (9:18364122 C>T), RS1000017892 (9:18118853 C>T), RS1000027095 (9:18617842 C>G,T), RS1000029845 (9:18136437 A>G), RS1000032987 (9:18329746 A>G), RS1000033625 (9:18144172 C>T), RS1000037391 (9:18227578 T>C), RS1000038541 (9:17915218 A>G), RS1000039638 (9:18796822 A>G), RS1000040383 (9:18402497 C>G,T), RS1000041387 (9:18532657 A>C,G), RS1000046261 (9:18401900 A>C,T)

Disease associations

OMIM: gene MIM:609198 | disease phenotypes: MIM:158170, MIM:119530

GenCC curated gene-disease

Mondo (2): chromosome 9p deletion syndrome (MONDO:0008013), orofacial cleft 1 (MONDO:0007335)

Orphanet (1): Monosomy 9p syndrome (Orphanet:261112)

HPO phenotypes

27 total (27 of 27 shown, HPO-id order):

HPO	Term
HP:0000077	Abnormality of the kidney
HP:0000248	Brachycephaly
HP:0000252	Microcephaly
HP:0000303	Mandibular prognathia
HP:0000321	Square face
HP:0000322	Short philtrum
HP:0000400	Macrotia
HP:0000431	Wide nasal bridge
HP:0000541	Retinal detachment
HP:0000545	Myopia
HP:0000557	Buphthalmos
HP:0000558	Rieger anomaly
HP:0000696	Delayed eruption of permanent teeth
HP:0000787	Nephrolithiasis
HP:0000851	Congenital hypothyroidism
HP:0001182	Tapered finger
HP:0001848	Calcaneovalgus deformity
HP:0002076	Migraine
HP:0005487	Prominent metopic ridge
HP:0005990	Thyroid hypoplasia
HP:0008007	Primary congenital glaucoma
HP:0008619	Bilateral sensorineural hearing impairment
HP:0010490	Abnormality of the palmar creases
HP:0010804	Tented upper lip vermilion
HP:0012448	Delayed myelination
HP:0020038	Vertebrobasilar dolichoectasia
HP:0100807	Long fingers

GWAS associations

30 associations (top):

Study	Trait	p-value
GCST001343_12	Fat distribution (HIV)	3.000000e-06
GCST001762_337	Obesity-related traits	9.000000e-06
GCST001762_735	Obesity-related traits	9.000000e-06
GCST001890_5	QT interval (drug interaction)	8.000000e-06
GCST002337_86	Amyotrophic lateral sclerosis (sporadic)	2.000000e-06
GCST002641_3	Hip circumference (psychosocial stress interaction)	8.000000e-06
GCST003997_2	Myopia	2.000000e-14
GCST004285_4	Midgestational circulating levels of PBDEs	3.000000e-08
GCST004294_10	Nicotine dependence	5.000000e-06
GCST004746_19	Small cell lung carcinoma	9.000000e-07
GCST004864_2	Perceived unattractiveness to mosquitoes	7.000000e-06
GCST006190_81	Diastolic blood pressure x smoking status (ever vs never) interaction (2df test)	4.000000e-08
GCST006192_43	Systolic blood pressure x smoking status (ever vs never) interaction (2df test)	3.000000e-06
GCST006223_3	Cerebral cortical growth	5.000000e-06
GCST006291_28	Spherical equivalent or myopia (age of diagnosis)	2.000000e-13
GCST006427_8	Depression in smokers	2.000000e-06
GCST006979_159	Heel bone mineral density	3.000000e-09
GCST006979_160	Heel bone mineral density	6.000000e-17
GCST007743_20	Iris color (L* coordinate)	5.000000e-06
GCST008158_33	Body mass index	6.000000e-06
GCST008477_37	Emphysema annual change measurement in smokers (adjusted lung density)	6.000000e-06
GCST009220_6	Corpus callosum anterior volume	2.000000e-06
GCST009391_861	Metabolite levels	8.000000e-06
GCST009724_15	Vertical cup-disc ratio (multi-trait analysis)	2.000000e-11
GCST010002_316	Refractive error	4.000000e-51
GCST011687_7	Systolic blood pressure	8.000000e-07
GCST011743_80	HDL cholesterol levels in HIV infection	1.000000e-07
GCST90000025_467	Appendicular lean mass	3.000000e-09
GCST90011900_213	Serum alkaline phosphatase levels	6.000000e-10
GCST90013406_134	Liver enzyme levels (alkaline phosphatase)	3.000000e-11

EFO canonical traits (21, from GWAS)

EFO ID	Trait name
EFO:0004341	body fat distribution
EFO:0005106	body composition measurement
EFO:0004682	QT interval
EFO:0006783	psychosocial stress measurement
EFO:0007961	polybrominated biphenyl measurement
EFO:0007962	polybrominated diphenyl ether measurement
EFO:0007964	gestational serum measurement
EFO:0008380	perceived unattractiveness to mosquitos measurement
EFO:0006336	diastolic blood pressure
EFO:0006527	smoking status measurement
EFO:0006335	systolic blood pressure
EFO:0004847	age at onset
EFO:0009270	heel bone mineral density
EFO:0009764	eye colour measurement
EFO:0004340	body mass index
EFO:0007626	emphysema imaging measurement
EFO:0010533	sorbitol measurement
EFO:0006939	cup-to-disc ratio measurement
EFO:0004612	high density lipoprotein cholesterol measurement
EFO:0004980	appendicular lean mass
EFO:0004533	alkaline phosphatase measurement

MeSH disease descriptors (2)

Descriptor	Name	Tree numbers
C538024	Chromosome 9p Deletion Syndrome (supp.)
C566121	Orofacial Cleft 1 (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
bisphenol A	affects cotreatment, increases methylation, decreases expression	2
Arsenic	affects methylation, affects cotreatment, increases abundance, increases expression	2
Valproic Acid	increases expression, increases methylation	2
GSK-J4	increases expression	1
bisphenol F	affects cotreatment, decreases expression	1
ethyl-p-hydroxybenzoate	decreases expression	1
arsenite	increases methylation	1
sodium arsenite	increases abundance, increases expression, affects cotreatment	1
cobaltous chloride	decreases expression	1
manganese chloride	increases abundance, increases expression, affects cotreatment	1
benzo(e)pyrene	decreases methylation	1
nickel sulfate	decreases expression	1
perfluorooctane sulfonic acid	increases expression	1
2-palmitoylglycerol	increases expression	1
entinostat	increases expression	1
2,2’,4,4’,5-brominated diphenyl ether	decreases expression	1
bisphenol B	increases expression	1
abrine	increases expression	1
bisphenol S	affects cotreatment, decreases expression	1
(+)-JQ1 compound	decreases expression	1
bisphenol AF	increases expression	1
Resveratrol	decreases expression, affects cotreatment	1
Sunitinib	decreases expression	1
Fulvestrant	affects cotreatment, increases methylation	1
Benzo(a)pyrene	decreases expression	1
Dexamethasone	affects cotreatment, decreases expression	1
Doxorubicin	decreases expression	1
Endosulfan	increases expression	1
Estradiol	affects cotreatment, increases expression	1
Indomethacin	affects cotreatment, decreases expression	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT04586400	Not specified	RECRUITING	Chromosome 9 P Minus Syndrome