SPECC1

Summary

SPECC1 (sperm antigen with calponin homology and coiled-coil domains 1, HGNC:30615) is a protein-coding gene on chromosome 17p11.2, encoding Cytospin-B (Q5M775).

The protein encoded by this gene belongs to the cytospin-A family. It is localized in the nucleus, and highly expressed in testis and some cancer cell lines. A chromosomal translocation involving this gene and platelet-derived growth factor receptor, beta gene (PDGFRB) may be a cause of juvenile myelomonocytic leukemia. Alternatively spliced transcript variants encoding different isoforms have been described for this gene.

Source: NCBI Gene 92521 — RefSeq curated summary.

At a glance

• GWAS associations: 26
• Clinical variants (ClinVar): 204 total — 1 likely-pathogenic
• MANE Select transcript: NM_001243439

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:30615
Approved symbol	SPECC1
Name	sperm antigen with calponin homology and coiled-coil domains 1
Location	17p11.2
Locus type	gene with protein product
Status	Approved
Aliases	HCMOGT-1, FLJ36955, NSP
Ensembl gene	ENSG00000128487
Ensembl biotype	protein_coding
OMIM	608793
Entrez	92521

Gene structure

Transcript identifiers

Ensembl transcripts: 55 — 41 protein_coding, 7 nonsense_mediated_decay, 4 protein_coding_CDS_not_defined, 3 retained_intron

ENST00000261503, ENST00000395522, ENST00000395525, ENST00000395527, ENST00000395529, ENST00000395530, ENST00000467722, ENST00000472876, ENST00000492188, ENST00000578321, ENST00000579688, ENST00000580934, ENST00000581399, ENST00000581973, ENST00000582063, ENST00000582226, ENST00000583463, ENST00000583482, ENST00000583528, ENST00000584527, ENST00000676570, ENST00000676737, ENST00000677148, ENST00000677784, ENST00000677914, ENST00000678019, ENST00000678315, ENST00000678321, ENST00000678651, ENST00000679048, ENST00000679049, ENST00000679058, ENST00000679255, ENST00000679740, ENST00000679801, ENST00000679819, ENST00000680019, ENST00000680124, ENST00000680373, ENST00000680374, ENST00000680572, ENST00000680604, ENST00000680740, ENST00000680830, ENST00000681116, ENST00000681202, ENST00000681545, ENST00000681564, ENST00000681593, ENST00000681731, ENST00000681875, ENST00000851980, ENST00000851981, ENST00000965406, ENST00000965407

RefSeq mRNA: 15 — MANE Select: NM_001243439 NM_001033553, NM_001033554, NM_001033555, NM_001243438, NM_001243439, NM_001386077, NM_001386078, NM_001386079, NM_001386080, NM_001386081, NM_001386082, NM_001386083, NM_001386084, NM_001386085, NM_152904

CCDS: CCDS32590, CCDS42280, CCDS42281, CCDS45628, CCDS58531, CCDS92274, CCDS92275, CCDS92276, CCDS92277, CCDS92278, CCDS92279

Canonical transcript exons

ENST00000395527 — 15 exons

Exon	Start	End
ENSE00001018284	20306023	20306082
ENSE00001154697	20260192	20260294
ENSE00001154705	20257451	20257607
ENSE00001154735	20296961	20297077
ENSE00001314252	20204333	20205912
ENSE00001521958	20313976	20319026
ENSE00002332480	20247219	20247319
ENSE00002347306	20253505	20253586
ENSE00002350158	20245926	20246071
ENSE00003538827	20096631	20096798
ENSE00003572128	20231758	20231831
ENSE00003605360	20232200	20232405
ENSE00003663135	20110427	20110562
ENSE00003677583	20227413	20227620
ENSE00003914148	20009359	20009424

Expression profiles

Bgee: expression breadth ubiquitous, 213 present calls, max score 97.85.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 43.2940 / max 618.3238, expressed in 1757 samples.

FANTOM5 promoters (13 alternative TSS)

Promoter ID	TPM avg	Samples expressed
159870	28.7548	1590
159865	4.4119	541
159858	3.7586	608
159868	3.3249	1132
159869	0.9646	558
159860	0.7099	114
159871	0.4975	261
159866	0.2933	143
159863	0.1888	107
159864	0.1240	66

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
calcaneal tendon	UBERON:0003701	97.85	gold quality
corpus callosum	UBERON:0002336	95.71	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	93.95	gold quality
adrenal tissue	UBERON:0018303	93.78	gold quality
sural nerve	UBERON:0015488	93.50	gold quality
spinal cord	UBERON:0002240	93.40	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	92.85	gold quality
globus pallidus	UBERON:0001875	92.27	gold quality
medial globus pallidus	UBERON:0002477	92.24	gold quality
lateral globus pallidus	UBERON:0002476	92.04	gold quality
substantia nigra	UBERON:0002038	91.83	gold quality
midbrain	UBERON:0001891	91.41	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	91.13	gold quality
substantia nigra pars reticulata	UBERON:0001966	91.06	gold quality
stromal cell of endometrium	CL:0002255	91.03	gold quality
tendon	UBERON:0000043	91.01	gold quality
inferior vagus X ganglion	UBERON:0005363	90.49	gold quality
left testis	UBERON:0004533	90.31	gold quality
monocyte	CL:0000576	90.15	gold quality
subthalamic nucleus	UBERON:0001906	90.14	gold quality
amygdala	UBERON:0001876	90.05	gold quality
substantia nigra pars compacta	UBERON:0001965	89.88	gold quality
bone marrow cell	CL:0002092	89.83	gold quality
right testis	UBERON:0004534	89.80	gold quality
prefrontal cortex	UBERON:0000451	89.76	gold quality
lateral nuclear group of thalamus	UBERON:0002736	89.76	gold quality
Brodmann (1909) area 9	UBERON:0013540	89.73	gold quality
leukocyte	CL:0000738	89.60	gold quality
right frontal lobe	UBERON:0002810	89.57	gold quality
ascending aorta	UBERON:0001496	89.47	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	10.62
E-MTAB-6678	yes	5.62
E-MTAB-6142	no	42.78

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

127 targeting SPECC1, 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-3613-3P	100.00	76.36	7965
HSA-MIR-4510	100.00	66.60	2050
HSA-MIR-6127	100.00	66.76	2188
HSA-MIR-6129	100.00	66.46	2080
HSA-MIR-6130	100.00	66.69	2012
HSA-MIR-6133	100.00	66.48	2064
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-8485	100.00	77.57	4731
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-513B-5P	99.99	69.96	2150
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-3065-5P	99.97	71.56	3281
HSA-MIR-507	99.97	70.11	1915
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-4267	99.96	66.53	2368
HSA-MIR-557	99.96	70.01	1640
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-141-3P	99.94	72.79	2421
HSA-MIR-200A-3P	99.94	72.68	2420
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

Literature-anchored findings (GeneRIF, showing 4)

• PCR and fluoresecne in situ hybridization shows that HCMOGT-1 is a novel fusion partner to PDGFRB in juvenile myelomonocytic leukemia with t(5;17)(q33;p11.2). (PMID:15087372)
• NSP 5a3a’s novel interaction with B23 and ribonuclear protein hnRNP-L implicates NSP 5a3a in cellular processes such as ribosome biogenesis and rRNA transcription . (PMID:20237420)
• Loss of NSP 5a3a is associated with head and neck carcinoma. (PMID:21311098)
• NSP 5a3a induces apoptosis in Head and Neck cell line HN30 through p73-DAXX and TRAF2-TRADD. (PMID:22170762)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	specc1	ENSDARG00000029480
mus_musculus	Specc1	ENSMUSG00000042331
rattus_norvegicus	Specc1	ENSRNOG00000002903
drosophila_melanogaster	spdi	FBGN0025633

Paralogs (1): SPECC1L (ENSG00000100014)

Protein

Protein identifiers

Cytospin-B — Q5M775 (reviewed: Q5M775)

Alternative names: Nuclear structure protein 5, Sperm antigen HCMOGT-1, Sperm antigen with calponin homology and coiled-coil domains 1

All UniProt accessions (20): Q5M775, A0A7I2V416, A0A7I2V451, A0A7I2V486, A0A7I2V562, A0A7I2V5G2, A0A7I2YQJ3, A0A7P0T8Y6, A0A7P0T9K0, A0A7P0TAS3, A0A7P0TB87, A0A7P0TBD3, A0A7P0TBP2, A0A7P0Z4I1, J3KRB9, J3KRN9, J3KSG2, J3QKL1, J3QQM0, J3QS22

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Nucleus Membrane Membrane Membrane.

Tissue specificity. Highly expressed in testis. Barely detectable in other tissues. Also highly expressed in some cancer cell lines.

Disease relevance. A chromosomal aberration involving CYTSB may be a cause of juvenile myelomonocytic leukemia. Translocation t(5;17)(q33;p11.2) with PDGFRB.

Similarity. Belongs to the cytospin-A family.

Isoforms (5)

UniProt ID	Names	Canonical?
Q5M775-1	1, NSP5beta3beta	yes
Q5M775-2	2, NSP5beta3alpha
Q5M775-3	3, NSP5alpha3alpha
Q5M775-4	4, NSP5alpha3beta
Q5M775-5	5

RefSeq proteins (15): NP_001028725, NP_001028726, NP_001028727, NP_001230367, NP_001230368, NP_001373006, NP_001373007, NP_001373008, NP_001373009, NP_001373010, NP_001373011, NP_001373012, NP_001373013, NP_001373014, NP_690868 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001715	CH_dom	Domain
IPR036872	CH_dom_sf	Homologous_superfamily
IPR050540	F-actin_Monoox_Mical	Family

Pfam: PF00307

UniProt features (57 total): modified residue 19, compositionally biased region 9, sequence conflict 8, region of interest 5, splice variant 4, sequence variant 3, initiator methionine 3, lipid moiety-binding region 3, chain 1, domain 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5M775-F1	68.05	0.40

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 (22): 38, 55, 78, 112, 131, 134, 137, 138, 142, 218, 241, 361, 366, 369, 425, 847, 863, 912, 914, 2 …

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 176 (showing top): GOBP_EMBRYO_DEVELOPMENT_ENDING_IN_BIRTH_OR_EGG_HATCHING, GOBP_COGNITION, GOBP_BEHAVIOR, GOBP_ASSOCIATIVE_LEARNING, IVANOVA_HEMATOPOIESIS_MATURE_CELL, CAGCTG_AP4_Q5, GOCC_MICROTUBULE_ORGANIZING_CENTER, MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_6, GOBP_IN_UTERO_EMBRYONIC_DEVELOPMENT, LE_EGR2_TARGETS_UP, GOBP_LEARNING, GOBP_BLASTOCYST_DEVELOPMENT, GOBP_EMBRYO_DEVELOPMENT, LINDVALL_IMMORTALIZED_BY_TERT_DN, RGAGGAARY_PU1_Q6

GO Biological Process (3): blastocyst development (GO:0001824), associative learning (GO:0008306), actin cytoskeleton organization (GO:0030036)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (9): fibrillar center (GO:0001650), nucleoplasm (GO:0005654), microtubule organizing center (GO:0005815), cytosol (GO:0005829), membrane (GO:0016020), filamentous actin (GO:0031941), apical part of cell (GO:0045177), nucleus (GO:0005634), cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	7
in utero embryonic development	1
anatomical structure development	1
learning	1
cytoskeleton organization	1
actin filament-based process	1
binding	1
nucleolus	1
nuclear lumen	1
microtubule cytoskeleton	1
cytoplasm	1
actin filament	1
protein-containing complex	1
intracellular membrane-bounded organelle	1
intracellular anatomical structure	1

Protein interactions and networks

STRING

824 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SPECC1	SH2D3C	Q8N5H7	927
SPECC1	SH2D3A	Q9BRG2	912
SPECC1	HDAC2	Q92769	903
SPECC1	PRSS57	Q6UWY2	874
SPECC1	SMC1A	Q14683	715
SPECC1	MRPL58	Q14197	712
SPECC1	PPP1CA	P08129	678
SPECC1	KIR2DL4	P78400	620
SPECC1	PDGFRB	P09619	539
SPECC1	NTRK1	P04629	512
SPECC1	ISG15	P05161	508
SPECC1	BAG6	P46379	506
SPECC1	OAS3	Q9Y6K5	450
SPECC1	ACE2	Q9BYF1	446
SPECC1	BRCA1	P38398	443

IntAct

112 interactions, top by confidence:

A	B	Type	Score
RBBP5	KMT2D	psi-mi:“MI:0914”(association)	0.840
KRT31	HGS	psi-mi:“MI:0914”(association)	0.780
CFTR	ESYT2	psi-mi:“MI:2364”(proximity)	0.710
WDR5	MEN1	psi-mi:“MI:0914”(association)	0.710
YWHAG	BLTP3B	psi-mi:“MI:2364”(proximity)	0.640
YWHAH	BLTP3B	psi-mi:“MI:2364”(proximity)	0.570
KSR2	POLR3A	psi-mi:“MI:0914”(association)	0.530
SLC25A41	NUDT19	psi-mi:“MI:0914”(association)	0.530
YWHAZ	BLTP3B	psi-mi:“MI:0914”(association)	0.530
PCDHGB1	FAM171A2	psi-mi:“MI:0914”(association)	0.530
NUP62	RGPD8	psi-mi:“MI:0914”(association)	0.530
PCDHAC2	TMEM223	psi-mi:“MI:0914”(association)	0.530
NRAS	ESYT2	psi-mi:“MI:2364”(proximity)	0.480
Cdk1		psi-mi:“MI:0915”(physical association)	0.400
Poc1b		psi-mi:“MI:0915”(physical association)	0.400
Erh	BCLAF3	psi-mi:“MI:0915”(physical association)	0.400
Stag2	PPP1R12A	psi-mi:“MI:0915”(physical association)	0.400
Mau2	NIPBL	psi-mi:“MI:0915”(physical association)	0.400
Trim69		psi-mi:“MI:0915”(physical association)	0.400
SPECC1	FXR1	psi-mi:“MI:0915”(physical association)	0.370
MYH9	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
ANLN	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
MYO18A	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
MYO1C	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
MYO19	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
ATP6AP2	TMUB1	psi-mi:“MI:0914”(association)	0.350
FLNA	PLEKHG3	psi-mi:“MI:0914”(association)	0.350

BioGRID (195): SPECC1 (Affinity Capture-RNA), SPECC1 (Affinity Capture-MS), SPECC1 (Affinity Capture-MS), SPECC1 (Affinity Capture-MS), SPECC1 (Affinity Capture-MS), SPECC1 (Affinity Capture-MS), SPECC1 (Affinity Capture-MS), SPECC1 (Affinity Capture-MS), SPECC1 (Affinity Capture-MS), SPECC1 (Affinity Capture-MS), SPECC1 (Affinity Capture-MS), SPECC1 (Affinity Capture-MS), SPECC1 (Affinity Capture-MS), SPECC1 (Affinity Capture-MS), SPECC1 (Affinity Capture-MS)

ESM2 similar proteins: A0A287B8J2, A6QR54, A8IQT2, A8WUP2, C5E2E7, C9ZN16, G5ECG0, O08788, O16844, O48791, O55156, P13496, P28023, P35458, P45970, P54623, Q01397, Q14203, Q17695, Q23529, Q292S8, Q2KN93, Q2KN94, Q2KN95, Q2KN96, Q2KN97, Q2KN98, Q2KN99, Q2KNA0, Q2KNA1, Q3SWS9, Q585H6, Q5B993, Q5DTN8, Q5M775, Q5SXY1, Q5VZ66, Q69YQ0, Q6PCJ1, Q75EN7

Diamond homologs: A5D7D1, A8MU46, D3ZEN0, D3ZHV2, D3ZQL6, D4A1F2, E1BBG2, E7F9T0, F1MF74, F1QH17, F1QWK4, F1RA39, F6QZ15, G3MWR8, G3V7L1, L7UZ85, M9MRD1, O13728, O15020, O43707, O76329, O88990, O94851, O97592, P05094, P05095, P11277, P11530, P11531, P11532, P11533, P12814, P15508, P18091, P20111, P30427, P35609, P46939, P53814, P57780

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 126 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
Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex	8	68.0×	1e-11
Activation of BAD and translocation to mitochondria	7	67.5×	3e-10
SARS-CoV-1 targets host intracellular signalling and regulatory pathways	7	59.5×	8e-10
RHO GTPases activate PKNs	11	44.2×	3e-13
Activation of BH3-only proteins	7	44.0×	9e-09
RHO GTPases activate PAKs	6	41.3×	2e-07
Signaling by FLT3 fusion proteins	5	36.1×	6e-06
Intrinsic Pathway for Apoptosis	7	25.9×	4e-07

GO biological processes:

GO term	Partners	Fold	FDR
protein targeting	5	18.9×	2e-03
intracellular protein localization	10	10.8×	3e-05
Ras protein signal transduction	5	10.6×	1e-02
MAPK cascade	6	9.5×	5e-03
actin filament organization	7	8.6×	4e-03
actin cytoskeleton organization	8	6.5×	4e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	1
Uncertain significance	167
Likely benign	9
Benign	2

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
1801728	NM_001243439.2(SPECC1):c.1747A>G (p.Met583Val)	Likely pathogenic

SpliceAI

4473 predictions. Top by Δscore:

Variant	Effect	Δscore
17:20096752:GTTC:G	donor_gain	1.0000
17:20096753:TTCT:T	donor_gain	1.0000
17:20096794:GCAGG:G	donor_gain	1.0000
17:20110416:A:AG	acceptor_gain	1.0000
17:20110417:A:AG	acceptor_gain	1.0000
17:20110418:C:G	acceptor_gain	1.0000
17:20110425:A:AG	acceptor_gain	1.0000
17:20110426:G:GT	acceptor_gain	1.0000
17:20110426:GCTC:G	acceptor_gain	1.0000
17:20110426:GCTCA:G	acceptor_gain	1.0000
17:20227406:A:AG	acceptor_gain	1.0000
17:20227408:TTTA:T	acceptor_loss	1.0000
17:20227410:TA:T	acceptor_loss	1.0000
17:20227411:A:AG	acceptor_gain	1.0000
17:20227411:A:C	acceptor_loss	1.0000
17:20227411:AGGT:A	acceptor_gain	1.0000
17:20227411:AGGTG:A	acceptor_gain	1.0000
17:20227412:G:GA	acceptor_gain	1.0000
17:20227412:GGT:G	acceptor_gain	1.0000
17:20227412:GGTG:G	acceptor_gain	1.0000
17:20227412:GGTGG:G	acceptor_gain	1.0000
17:20227609:G:GG	donor_gain	1.0000
17:20227617:GAAA:G	donor_gain	1.0000
17:20227621:G:GG	donor_gain	1.0000
17:20231753:TCTA:T	acceptor_loss	1.0000
17:20231756:A:AG	acceptor_gain	1.0000
17:20231756:A:C	acceptor_loss	1.0000
17:20231757:G:GA	acceptor_loss	1.0000
17:20231757:G:GG	acceptor_gain	1.0000
17:20231757:GGT:G	acceptor_gain	1.0000

AlphaMissense

6982 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
17:20232237:T:C	L728P	1.000
17:20260247:C:A	R965S	1.000
17:20260257:T:C	L968P	1.000
17:20260260:T:C	L969P	1.000
17:20260265:T:A	W971R	1.000
17:20260265:T:C	W971R	1.000
17:20260267:G:C	W971C	1.000
17:20260267:G:T	W971C	1.000
17:20260270:C:G	C972W	1.000
17:20296978:T:A	N986K	1.000
17:20296978:T:G	N986K	1.000
17:20296979:T:C	F987L	1.000
17:20296980:T:C	F987S	1.000
17:20296981:C:A	F987L	1.000
17:20296981:C:G	F987L	1.000
17:20296991:T:A	W991R	1.000
17:20296991:T:C	W991R	1.000
17:20296993:G:C	W991C	1.000
17:20296993:G:T	W991C	1.000
17:20297001:G:A	G994D	1.000
17:20314012:T:A	W1052R	1.000
17:20314012:T:C	W1052R	1.000
17:20314014:G:C	W1052C	1.000
17:20314014:G:T	W1052C	1.000
17:20205221:T:C	L391P	0.999
17:20205226:G:C	A393P	0.999
17:20232215:T:A	W721R	0.999
17:20232215:T:C	W721R	0.999
17:20232224:T:C	F724L	0.999
17:20232225:T:C	F724S	0.999

dbSNP variants (sampled 300 via entrez): RS1000029220 (17:20192352 A>C), RS1000032559 (17:20107578 T>C), RS1000053171 (17:20157787 A>G), RS1000057741 (17:20187771 C>A,T), RS1000064608 (17:20058528 G>A,T), RS1000070621 (17:20195396 A>G), RS1000075106 (17:20018779 G>A), RS1000075424 (17:20152070 G>A), RS1000088451 (17:20188022 A>G,T), RS1000108687 (17:20312661 G>A), RS1000109022 (17:20273480 A>G), RS1000112208 (17:20019500 G>A), RS1000128787 (17:20207514 C>T), RS1000129786 (17:20268999 C>T), RS1000133660 (17:20227772 G>A,C)

Disease associations

OMIM: gene MIM:608793 | disease phenotypes:

GenCC curated gene-disease

Mondo (1): myoepithelial tumor (MONDO:0002380)

Orphanet (0):

HPO phenotypes

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

GWAS associations

26 associations (top):

Study	Trait	p-value
GCST001762_409	Obesity-related traits	9.000000e-06
GCST004602_289	Mean corpuscular volume	4.000000e-37
GCST004611_214	High light scatter reticulocyte count	2.000000e-15
GCST004612_204	High light scatter reticulocyte percentage of red cells	4.000000e-13
GCST004628_14	Immature fraction of reticulocytes	8.000000e-09
GCST004630_211	Mean corpuscular hemoglobin	6.000000e-39
GCST004946_7	Schizophrenia	4.000000e-08
GCST007201_253	Schizophrenia	1.000000e-08
GCST007201_405	Schizophrenia	9.000000e-07
GCST010083_224	Hemoglobin levels	1.000000e-10
GCST010703_51	Brain morphology (MOSTest)	1.000000e-08
GCST90002384_407	Hemoglobin	6.000000e-10
GCST90002385_88	High light scatter reticulocyte count	1.000000e-35
GCST90002386_178	High light scatter reticulocyte percentage of red cells	6.000000e-28
GCST90002387_22	Immature fraction of reticulocytes	3.000000e-18
GCST90002390_106	Mean corpuscular hemoglobin	8.000000e-30
GCST90002392_10	Mean corpuscular volume	6.000000e-43
GCST90002392_9	Mean corpuscular volume	3.000000e-09
GCST90002396_610	Mean reticulocyte volume	5.000000e-42
GCST90002396_611	Mean reticulocyte volume	8.000000e-10
GCST90002397_735	Mean spheric corpuscular volume	2.000000e-59
GCST90002397_736	Mean spheric corpuscular volume	1.000000e-12
GCST90002397_737	Mean spheric corpuscular volume	2.000000e-09
GCST90002403_353	Red blood cell count	3.000000e-15
GCST90002405_330	Reticulocyte count	1.000000e-33
GCST90002406_451	Reticulocyte fraction of red cells	5.000000e-26

EFO canonical traits (7, from GWAS)

EFO ID	Trait name
EFO:0005190	urinary nitrogen measurement
EFO:0007986	reticulocyte count
EFO:0004527	mean corpuscular hemoglobin
EFO:0004509	hemoglobin measurement
EFO:0004346	neuroimaging measurement
EFO:0010701	mean reticulocyte volume
EFO:0004305	erythrocyte count

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D009208	Myoepithelioma	C04.557.435.585

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
bisphenol A	increases expression, affects cotreatment, decreases methylation	3
Benzo(a)pyrene	decreases expression, decreases methylation, increases expression	3
Valproic Acid	affects cotreatment, increases expression	3
sodium arsenite	decreases expression, increases expression	2
Tobacco Smoke Pollution	increases expression	2
FR900359	affects phosphorylation	1
triphenyl phosphate	affects expression	1
sodium arsenate	decreases expression	1
arsenite	affects binding, decreases reaction	1
1,6-hexamethylene diisocyanate	increases methylation	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
potassium chromate(VI)	decreases expression	1
aflatoxin B2	increases methylation	1
coumarin	affects phosphorylation	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression, affects cotreatment, decreases expression	1
di-n-butylphosphoric acid	affects expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
dorsomorphin	affects cotreatment, increases expression	1
Fulvestrant	affects cotreatment, decreases methylation	1
Acetaminophen	increases expression	1
Vehicle Emissions	decreases expression, increases abundance	1
Caffeine	decreases phosphorylation	1
Calcitriol	increases expression, affects cotreatment	1
Diethylhexyl Phthalate	increases expression	1
Lipopolysaccharides	affects response to substance, increases expression, affects cotreatment, decreases expression	1
Smoke	decreases expression	1
Testosterone	affects cotreatment, increases expression	1
Dronabinol	increases expression	1
Thimerosal	increases expression	1
Thiram	increases expression	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT03600649	PHASE1	UNKNOWN	Clinical Trial of SP-2577 (Seclidemstat) in Patients With Relapsed or Refractory Ewing or Ewing-related Sarcomas
NCT05266196	PHASE1/PHASE2	UNKNOWN	A Rollover Protocol to Allow for Continued Access to the LSD1 Inhibitor Seclidemstat (SP-2577)
NCT06239272	PHASE1/PHASE2	RECRUITING	NRSTS2021, A Risk Adapted Study Evaluating Maintenance Pazopanib, Limited Margin, Dose-Escalated Radiation Therapy and Selinexor in Non-Rhabdomyosarcoma Soft Tissue Sarcoma (NRSTS)
NCT06625190	PHASE1/PHASE2	RECRUITING	Alpha/Beta T and B Cell Depletion With Zoledronic Acid for Solid Tumors
NCT06244420	Not specified	COMPLETED	Malignant Myoepithelioma of Bone and Soft Tissues: Diagnostic Imaging and Histology in Relation to Prognosis