ZNF638

Summary

ZNF638 (zinc finger protein 638, HGNC:17894) is a protein-coding gene on chromosome 2p13.3-p13.2, encoding Zinc finger protein 638 (Q14966). Transcription factor that binds to cytidine clusters in double-stranded DNA. It is a selective cancer dependency (DepMap: 10.1% of cell lines).

The protein encoded by this gene is a nucleoplasmic protein. It binds cytidine-rich sequences in double-stranded DNA. This protein has three types of domains: MH1, MH2 (repeated three times) and MH3. It is associated with packaging, transferring, or processing transcripts. Multiple alternatively spliced transcript variants have been found for this gene, but the biological validity of some variants has not been determined.

Source: NCBI Gene 27332 — RefSeq curated summary.

At a glance

• GWAS associations: 27
• Clinical variants (ClinVar): 331 total
• Cancer dependency (DepMap): dependent in 10.1% of screened cell lines
• MANE Select transcript: NM_014497

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:17894
Approved symbol	ZNF638
Name	zinc finger protein 638
Location	2p13.3-p13.2
Locus type	gene with protein product
Status	Approved
Aliases	NP220, MGC26130, Zfp638
Ensembl gene	ENSG00000075292
Ensembl biotype	protein_coding
OMIM	614349
Entrez	27332

Gene structure

Transcript identifiers

Ensembl transcripts: 37 — 24 protein_coding, 9 retained_intron, 3 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000264447, ENST00000409407, ENST00000409544, ENST00000410075, ENST00000417778, ENST00000437658, ENST00000454122, ENST00000454278, ENST00000455226, ENST00000460310, ENST00000461991, ENST00000464375, ENST00000466330, ENST00000466975, ENST00000472758, ENST00000475743, ENST00000483421, ENST00000486494, ENST00000487638, ENST00000487707, ENST00000488126, ENST00000491843, ENST00000492262, ENST00000493576, ENST00000494241, ENST00000494621, ENST00000601581, ENST00000718085, ENST00000718086, ENST00000718087, ENST00000892310, ENST00000892311, ENST00000919370, ENST00000919371, ENST00000919372, ENST00000919373, ENST00000919374

RefSeq mRNA: 4 — MANE Select: NM_014497 NM_001014972, NM_001252612, NM_001252613, NM_014497

CCDS: CCDS1917

Canonical transcript exons

ENST00000264447 — 28 exons

Exon	Start	End
ENSE00001680685	71331782	71331875
ENSE00003697641	71363954	71364252
ENSE00003697653	71380513	71380565
ENSE00003697696	71363153	71363191
ENSE00003699636	71355719	71355780
ENSE00003755995	71380222	71380280
ENSE00003757611	71368382	71368528
ENSE00003758867	71365429	71365706
ENSE00003760065	71369883	71370005
ENSE00004034068	71431327	71431428
ENSE00004034069	71434742	71435061
ENSE00004034070	71348753	71350271
ENSE00004034071	71426460	71427414
ENSE00004034072	71400478	71400518
ENSE00004034074	71406128	71406262
ENSE00004034075	71408122	71408247
ENSE00004034077	71400112	71400180
ENSE00004034079	71418602	71418639
ENSE00004034080	71424650	71424715
ENSE00004034081	71405601	71405642
ENSE00004034082	71403870	71403998
ENSE00004034083	71401956	71402087
ENSE00004034084	71422814	71424038
ENSE00004034085	71428547	71428651
ENSE00004034088	71433165	71433283
ENSE00004034089	71396141	71396191
ENSE00004034090	71398701	71398772
ENSE00004034091	71399559	71399645

Expression profiles

Bgee: expression breadth ubiquitous, 300 present calls, max score 99.12.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 53.2588 / max 748.2458, expressed in 1815 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
20886	46.7866	1813
20884	6.4722	921

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
calcaneal tendon	UBERON:0003701	99.12	gold quality
corpus callosum	UBERON:0002336	98.77	gold quality
cerebellar hemisphere	UBERON:0002245	98.68	gold quality
cerebellar cortex	UBERON:0002129	98.62	gold quality
right hemisphere of cerebellum	UBERON:0014890	98.61	gold quality
adenohypophysis	UBERON:0002196	98.35	gold quality
ventricular zone	UBERON:0003053	98.30	gold quality
pituitary gland	UBERON:0000007	98.26	gold quality
right uterine tube	UBERON:0001302	98.26	gold quality
peripheral nervous system	UBERON:0000010	98.19	gold quality
tibial nerve	UBERON:0001323	98.19	gold quality
cerebellum	UBERON:0002037	98.13	gold quality
colonic epithelium	UBERON:0000397	98.12	gold quality
sural nerve	UBERON:0015488	98.00	gold quality
right ovary	UBERON:0002118	97.99	gold quality
left ovary	UBERON:0002119	97.99	gold quality
tendon	UBERON:0000043	97.97	gold quality
adrenal tissue	UBERON:0018303	97.92	gold quality
ganglionic eminence	UBERON:0004023	97.78	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	97.78	gold quality
mucosa of stomach	UBERON:0001199	97.73	gold quality
right testis	UBERON:0004534	97.72	gold quality
trigeminal ganglion	UBERON:0001675	97.69	gold quality
endocervix	UBERON:0000458	97.68	gold quality
nucleus accumbens	UBERON:0001882	97.65	gold quality
superior surface of tongue	UBERON:0007371	97.65	gold quality
right lobe of thyroid gland	UBERON:0001119	97.64	gold quality
cortical plate	UBERON:0005343	97.62	gold quality
caudate nucleus	UBERON:0001873	97.58	gold quality
left lobe of thyroid gland	UBERON:0001120	97.56	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	10.60

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

34 targeting ZNF638, 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-548C-3P	99.99	74.01	7587
HSA-LET-7F-2-3P	99.98	70.98	2588
HSA-MIR-1185-1-3P	99.98	71.04	2593
HSA-MIR-1185-2-3P	99.98	71.04	2593
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-551B-5P	99.96	71.28	3493
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-493-5P	99.96	72.47	2382
HSA-LET-7C-3P	99.95	73.42	2862
HSA-MIR-101-3P	99.94	75.03	2230
HSA-MIR-144-3P	99.94	73.98	2698
HSA-MIR-7-1-3P	99.91	71.53	4384
HSA-MIR-7-2-3P	99.91	71.40	4394
HSA-LET-7A-2-3P	99.87	70.53	1921
HSA-LET-7G-3P	99.85	70.43	1929
HSA-MIR-4719	99.73	72.10	3329
HSA-MIR-4729	99.69	72.18	4233
HSA-MIR-4502	99.65	66.99	1021
HSA-MIR-3682-3P	99.58	67.63	865
HSA-MIR-2115-3P	99.31	69.68	2026
HSA-MIR-8065	99.19	70.38	1289
HSA-MIR-4801	98.96	69.42	2096
HSA-MIR-6715B-3P	98.80	68.07	1204
HSA-MIR-6895-3P	98.79	65.69	996
HSA-MIR-519A-2-5P	98.78	71.74	1401
HSA-MIR-520B-5P	98.78	71.74	1401
HSA-MIR-4731-3P	98.56	68.60	1860
HSA-MIR-6872-3P	97.08	66.99	750

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 10.1% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 4)

• ZNF638 is a novel and early regulator of adipogenesis that works as a transcription cofactor of C/EBPs. (PMID:21602272)
• NP220 is the key protein that recruits the HUSH complex, SETDB1 and the histone deacetylases HDAC1 and HDAC4 to silence the unintegrated retroviral DNA; knockout of NP220 accelerates the replication of retroviruses; these experiments identify the molecular machinery that silences extrachromosomal retroviral DNA (PMID:30487602)
• USP7 mediates pathological hepatic de novo lipogenesis through promoting stabilization and transcription of ZNF638. (PMID:33040080)
• Epigenetic Silencing of Recombinant Adeno-associated Virus Genomes by NP220 and the HUSH Complex. (PMID:34878926)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	si:ch211-89o9.4	ENSDARG00000093237
danio_rerio	znf638	ENSDARG00000104169
mus_musculus	Zfp638	ENSMUSG00000030016
rattus_norvegicus	Zfp638	ENSRNOG00000014501

Paralogs (1): MATR3 (ENSG00000015479)

Protein

Protein identifiers

Zinc finger protein 638 — Q14966 (reviewed: Q14966)

Alternative names: Cutaneous T-cell lymphoma-associated antigen se33-1, Nuclear protein 220, Zinc finger matrin-like protein

All UniProt accessions (12): Q14966, A0A096LNQ0, A0A096LNR2, A0A096LNS4, A0A096LNX0, A0A096LPB4, A0A096LPI0, A0A096LPK8, C9JHV0, C9JMR2, C9JSD0, C9JWN0

UniProt curated annotations — full annotation on UniProt →

Function. Transcription factor that binds to cytidine clusters in double-stranded DNA. Plays a key role in the silencing of unintegrated retroviral DNA: some part of the retroviral DNA formed immediately after infection remains unintegrated in the host genome and is transcriptionally repressed. Mediates transcriptional repression of unintegrated viral DNA by specifically binding to the cytidine clusters of retroviral DNA and mediating the recruitment of chromatin silencers, such as the HUSH complex, SETDB1 and the histone deacetylases HDAC1 and HDAC4. Acts as an early regulator of adipogenesis by acting as a transcription cofactor of CEBPs (CEBPA, CEBPD and/or CEBPG), controlling the expression of PPARG and probably of other proadipogenic genes, such as SREBF1. May also regulate alternative splicing of target genes during adipogenesis.

Subunit / interactions. Interacts with FHL2. Interacts with CEBPA, CEBPD and CEBPG. Interacts with MPHOSPH8 and TASOR components of the HUSH complex; leading to recruitment of the HUSH complex. Interacts with SETDB1. Interacts with HDAC1. Interacts with HDAC4.

Subcellular location. Nucleus speckle.

Domain organisation. The matrin-type zinc finger domain is required for localization to nuclear speckles.

Miscellaneous. Tumor-associated antigen found in several cutaneous T-cell lymphoma (CTCL), and in particular in mycosis fungoides patients and in Sezary syndrome patients. Broadly expressed.

Isoforms (6)

UniProt ID	Names	Canonical?
Q14966-1	1, Alpha	yes
Q14966-2	2
Q14966-3	3
Q14966-4	4
Q14966-5	5
Q14966-6	6

RefSeq proteins (4): NP_001014972, NP_001239541, NP_001239542, NP_055312* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000504	RRM_dom	Domain
IPR000690	Matrin/U1-C_Znf_C2H2	Domain
IPR003604	Matrin/U1-like-C_Znf_C2H2	Domain
IPR012677	Nucleotide-bd_a/b_plait_sf	Homologous_superfamily
IPR013087	Znf_C2H2_type	Domain
IPR022755	Znf_C2H2_jaz	Domain
IPR033096	ZNF638_RRM1/2	Domain
IPR035979	RBD_domain_sf	Homologous_superfamily
IPR036236	Znf_C2H2_sf	Homologous_superfamily

Pfam: PF00076, PF12171

UniProt features (87 total): compositionally biased region 18, modified residue 18, region of interest 10, sequence conflict 10, splice variant 8, cross-link 5, sequence variant 5, strand 4, helix 4, domain 2, chain 1, DNA-binding region 1, zinc finger region 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
6SXW	X-RAY DIFFRACTION	2.75

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q14966-F1	45.56	0.08

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 (23): 47, 49, 54, 128, 289, 299, 369, 383, 420, 552, 605, 614, 636, 1100, 1401, 1641, 1667, 1882, 292, 775 …

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-381340	Transcriptional regulation of white adipocyte differentiation

MSigDB gene sets: 129 (showing top): REACTOME_TRANSCRIPTIONAL_REGULATION_OF_WHITE_ADIPOCYTE_DIFFERENTIATION, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, YY1_02, DACOSTA_UV_RESPONSE_VIA_ERCC3_COMMON_DN, GOBP_RNA_SPLICING, KIM_GERMINAL_CENTER_T_HELPER_UP, CREBP1_01, BURTON_ADIPOGENESIS_12, MORF_PAPSS1, YNGTTNNNATT_UNKNOWN, GOBP_REGULATION_OF_RNA_SPLICING, GINESTIER_BREAST_CANCER_ZNF217_AMPLIFIED_DN, GCCATNTTG_YY1_Q6, GOCC_NUCLEAR_SPECK, GOCC_NUCLEAR_BODY

GO Biological Process (2): RNA splicing (GO:0008380), regulation of RNA splicing (GO:0043484)

GO Molecular Function (7): double-stranded DNA binding (GO:0003690), RNA binding (GO:0003723), mRNA binding (GO:0003729), zinc ion binding (GO:0008270), nucleic acid binding (GO:0003676), DNA binding (GO:0003677), metal ion binding (GO:0046872)

GO Cellular Component (4): nucleus (GO:0005634), nucleoplasm (GO:0005654), cytoplasm (GO:0005737), nuclear speck (GO:0016607)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
Adipogenesis	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
nucleic acid binding	2
cellular anatomical structure	2
RNA processing	1
RNA splicing	1
regulation of gene expression	1
regulation of primary metabolic process	1
DNA binding	1
RNA binding	1
transition metal ion binding	1
binding	1
cation binding	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
intracellular anatomical structure	1
nuclear ribonucleoprotein granule	1

Protein interactions and networks

STRING

2466 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF638	SETDB1	Q15047	555
ZNF638	CEBPD	P49716	527
ZNF638	HNRNPA2B1	P22626	526
ZNF638	TASOR	Q9UK61	512
ZNF638	ZNF346	Q9UL40	486
ZNF638	ZNF700	Q9H0M5	474
ZNF638	TMEM82	A0PJX8	450
ZNF638	ZNF768	Q9H5H4	447
ZNF638	ZNF395	Q9H8N7	446
ZNF638	PPHLN1	Q8NEY8	440
ZNF638	MPHOSPH8	Q99549	435
ZNF638	ZNF446	Q9NWS9	423
ZNF638	SPATA3	Q8NHX4	421
ZNF638	HDAC4	P56524	410
ZNF638	ENOX2	Q16206	408

IntAct

258 interactions, top by confidence:

A	B	Type	Score
MED4	MED19	psi-mi:“MI:0914”(association)	0.900
NEUROG3	GXYLT2	psi-mi:“MI:0914”(association)	0.640
LIN28A	IGF2BP3	psi-mi:“MI:0914”(association)	0.640
YWHAH	PLEKHG3	psi-mi:“MI:0914”(association)	0.610
NPM1	MPHOSPH10	psi-mi:“MI:0914”(association)	0.610
RBFA	METTL15	psi-mi:“MI:0914”(association)	0.530
E4F1	ZBTB24	psi-mi:“MI:0914”(association)	0.530
BHLHA15	RPLP0	psi-mi:“MI:0914”(association)	0.530
YWHAQ	IGLC7	psi-mi:“MI:0914”(association)	0.530
YWHAZ	BLTP3B	psi-mi:“MI:0914”(association)	0.530
RPS3	ZNF316	psi-mi:“MI:0914”(association)	0.530
JPH4	ZSWIM8	psi-mi:“MI:0914”(association)	0.530
NOL9	IPO5	psi-mi:“MI:0914”(association)	0.530
TNFRSF13B	TNFRSF10B	psi-mi:“MI:0914”(association)	0.530
CLEC3A	ZZEF1	psi-mi:“MI:0914”(association)	0.530
SRPK2	RRP9	psi-mi:“MI:0914”(association)	0.530
GTF3C2	C1QBP	psi-mi:“MI:0914”(association)	0.530
CPSF6	DDX39A	psi-mi:“MI:0914”(association)	0.480
ESR2	FBLL1	psi-mi:“MI:0914”(association)	0.460
H3C1	SMCHD1	psi-mi:“MI:2364”(proximity)	0.410
ZC3H7B	ZNF638	psi-mi:“MI:0915”(physical association)	0.400
RAD51AP2	ZNF638	psi-mi:“MI:0915”(physical association)	0.400
ZNF638		psi-mi:“MI:0915”(physical association)	0.370
NELFCD	ZNF638	psi-mi:“MI:0915”(physical association)	0.370
Ppp1cb	MYO1C	psi-mi:“MI:0914”(association)	0.350
Taf15	BTBD10	psi-mi:“MI:0914”(association)	0.350
MPHOSPH8	HCFC1	psi-mi:“MI:0914”(association)	0.350
MATR3	BCLAF3	psi-mi:“MI:0914”(association)	0.350
HNRNPA1	MATR3	psi-mi:“MI:0914”(association)	0.350

BioGRID (317): ZNF638 (Affinity Capture-MS), ZNF638 (Affinity Capture-MS), ZNF638 (Affinity Capture-MS), ZNF638 (Affinity Capture-MS), ZNF638 (Affinity Capture-MS), ZNF638 (Affinity Capture-MS), ZNF638 (Affinity Capture-MS), ZNF638 (Two-hybrid), ZNF638 (Two-hybrid), ZNF638 (Two-hybrid), KRTAP4-12 (Two-hybrid), ZNF638 (Two-hybrid), ZNF638 (Two-hybrid), ZNF638 (Two-hybrid), EFEMP2 (Two-hybrid)

ESM2 similar proteins: A0A1I8MUL8, A2AG58, A2AJT9, E9Q309, E9Q4F7, F4JC20, F4KDH9, O23372, O35698, O94687, P0DW16, P78332, Q01613, Q14966, Q17QQ9, Q27IV2, Q2T9M9, Q32KY7, Q32PP1, Q3UQS8, Q4R731, Q53FD0, Q5LJZ2, Q5PPL1, Q5R6I3, Q5T481, Q5VT06, Q60990, Q61464, Q6AYU0, Q6H7U2, Q6IMN6, Q6P9P0, Q6UB98, Q6UB99, Q86V48, Q8BYK8, Q8CH25, Q8IH18, Q8K2H1

Diamond homologs: E9PT37, O95758, P0DW16, P17225, P26599, Q00438, Q14966, Q29099, Q3UQS8, Q5T481, Q61464, Q66H20, Q8BHD7, Q8WN55, Q91Z31, Q9FGL9, Q9UKA9, Q9ULV3, Q9Z118, P43243, P43244, Q8K310

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 236 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	34.5×	1e-08
Activation of BAD and translocation to mitochondria	6	29.3×	1e-06
SARS-CoV-1 targets host intracellular signalling and regulatory pathways	6	25.8×	3e-06
Defective Intrinsic Pathway for Apoptosis	5	24.4×	3e-05
Diseases of programmed cell death	5	20.3×	7e-05
Activation of BH3-only proteins	6	19.1×	2e-05
RHO GTPases activate PKNs	9	18.3×	1e-07
Intrinsic Pathway for Apoptosis	7	13.1×	2e-05

GO biological processes:

GO term	Partners	Fold	FDR
negative regulation of mRNA splicing, via spliceosome	8	28.8×	2e-07
post-transcriptional regulation of gene expression	5	15.2×	3e-03
protein targeting	7	12.0×	4e-04
regulation of alternative mRNA splicing, via spliceosome	9	10.3×	8e-05
negative regulation of translation	10	9.2×	7e-05
intracellular protein localization	10	4.9×	5e-03
protein phosphorylation	15	4.8×	2e-04
RNA splicing	11	4.6×	5e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	268
Likely benign	17
Benign	4

Top pathogenic / likely-pathogenic (0)

SpliceAI

6176 predictions. Top by Δscore:

Variant	Effect	Δscore
2:71332915:TTC:T	donor_gain	1.0000
2:71355714:A:AG	acceptor_gain	1.0000
2:71355714:AATAG:A	acceptor_gain	1.0000
2:71355717:A:AG	acceptor_gain	1.0000
2:71355717:AGGA:A	acceptor_loss	1.0000
2:71355718:G:GG	acceptor_gain	1.0000
2:71355770:T:G	donor_gain	1.0000
2:71355781:G:GG	donor_gain	1.0000
2:71365428:GATA:G	acceptor_gain	1.0000
2:71368369:A:AG	acceptor_gain	1.0000
2:71368370:C:G	acceptor_gain	1.0000
2:71368374:A:AG	acceptor_gain	1.0000
2:71368375:A:G	acceptor_gain	1.0000
2:71368377:A:G	acceptor_gain	1.0000
2:71368379:TA:T	acceptor_loss	1.0000
2:71368380:A:AG	acceptor_gain	1.0000
2:71368381:G:GT	acceptor_gain	1.0000
2:71368381:GC:G	acceptor_gain	1.0000
2:71368381:GCTT:G	acceptor_gain	1.0000
2:71368381:GCTTC:G	acceptor_gain	1.0000
2:71368490:A:T	donor_gain	1.0000
2:71368525:AGAGG:A	donor_loss	1.0000
2:71368526:GAG:G	donor_gain	1.0000
2:71368527:AGGT:A	donor_loss	1.0000
2:71368529:G:C	donor_loss	1.0000
2:71369877:TTTTA:T	acceptor_loss	1.0000
2:71369880:TAGGC:T	acceptor_loss	1.0000
2:71369881:A:AG	acceptor_gain	1.0000
2:71369882:G:GG	acceptor_gain	1.0000
2:71369990:A:T	donor_gain	1.0000

AlphaMissense

13094 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:71349385:T:C	L144S	1.000
2:71349393:T:C	F147L	1.000
2:71349395:T:A	F147L	1.000
2:71349395:T:G	F147L	1.000
2:71349397:G:A	G148E	1.000
2:71349400:T:C	L149S	1.000
2:71349411:G:C	D153H	1.000
2:71349412:A:C	D153A	1.000
2:71349412:A:G	D153G	1.000
2:71349415:T:A	L154Q	1.000
2:71349415:T:C	L154P	1.000
2:71349424:T:A	L157H	1.000
2:71349424:T:C	L157P	1.000
2:71349424:T:G	L157R	1.000
2:71349448:T:C	L165P	1.000
2:71349463:T:G	M170R	1.000
2:71349475:T:C	L174S	1.000
2:71349475:T:G	L174W	1.000
2:71350236:T:C	C428R	1.000
2:71350237:G:A	C428Y	1.000
2:71350238:T:G	C428W	1.000
2:71350245:T:C	C431R	1.000
2:71350247:T:G	C431W	1.000
2:71355722:T:A	W441R	1.000
2:71355722:T:C	W441R	1.000
2:71355724:G:C	W441C	1.000
2:71355724:G:T	W441C	1.000
2:71363163:T:A	W464R	1.000
2:71363163:T:C	W464R	1.000
2:71433200:T:C	C1930R	1.000

dbSNP variants (sampled 300 via entrez): RS1000000668 (2:71430891 T>A,C), RS1000035970 (2:71345380 C>T), RS1000040887 (2:71389348 T>A,C), RS1000056331 (2:71384261 T>C), RS1000107526 (2:71346745 T>C), RS1000112547 (2:71390243 C>T), RS1000190140 (2:71349238 A>G), RS1000196278 (2:71426062 G>A), RS1000203633 (2:71386904 G>A), RS1000207864 (2:71351205 A>C), RS1000251287 (2:71359716 T>A), RS1000292211 (2:71431513 A>C), RS1000390140 (2:71420695 G>GGC), RS1000473466 (2:71380720 A>T), RS1000474022 (2:71370219 C>T)

Disease associations

OMIM: gene MIM:614349 | disease phenotypes:

GenCC curated gene-disease

Mondo (1): breast ductal adenocarcinoma (MONDO:0005590)

Orphanet (0):

HPO phenotypes

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

GWAS associations

27 associations (top):

Study	Trait	p-value
GCST001885_4	Height	2.000000e-10
GCST002647_78	Height	3.000000e-13
GCST002702_5	Height	8.000000e-19
GCST004033_15	QRS interval (sulfonylurea treatment interaction)	4.000000e-08
GCST004364_17	Intelligence	4.000000e-06
GCST004364_35	Intelligence	5.000000e-08
GCST004635_4	Testicular germ cell tumor	2.000000e-11
GCST005142_23	Cognitive ability	2.000000e-08
GCST006268_495	Reaction time	4.000000e-08
GCST006288_232	Heel bone mineral density	8.000000e-07
GCST006288_575	Heel bone mineral density	2.000000e-10
GCST006979_12	Heel bone mineral density	2.000000e-11
GCST007044_5	Extremely high intelligence	6.000000e-09
GCST007096_21	Pulse pressure	6.000000e-09
GCST007269_71	Pulse pressure	2.000000e-09
GCST008156_11	Hip circumference adjusted for BMI	2.000000e-07
GCST008595_52	Cognitive ability, years of educational attainment or schizophrenia (pleiotropy)	5.000000e-12
GCST008839_25	Height	1.000000e-27
GCST012227_1198	Hip circumference adjusted for BMI	5.000000e-08
GCST012227_1199	Hip circumference adjusted for BMI	4.000000e-13
GCST90002388_73	Lymphocyte count	1.000000e-09
GCST90002390_364	Mean corpuscular hemoglobin	1.000000e-09
GCST90002392_206	Mean corpuscular volume	1.000000e-15
GCST90002396_214	Mean reticulocyte volume	1.000000e-18
GCST90002397_808	Mean spheric corpuscular volume	2.000000e-21
GCST90011899_16	Aspartate aminotransferase levels	2.000000e-10
GCST90020028_61	Hip circumference adjusted for BMI	5.000000e-12

EFO canonical traits (11, from GWAS)

EFO ID	Trait name
EFO:0007922	response to sulfonylurea
EFO:0004337	intelligence
EFO:0008393	reaction time measurement
EFO:0009270	heel bone mineral density
EFO:0005763	pulse pressure measurement
EFO:0008039	BMI-adjusted hip circumference
EFO:0004784	self reported educational attainment
EFO:0004587	lymphocyte count
EFO:0004527	mean corpuscular hemoglobin
EFO:0010701	mean reticulocyte volume
EFO:0004736	aspartate aminotransferase measurement

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D018270	Carcinoma, Ductal, Breast	C04.557.470.200.025.232.500; C04.557.470.615.132.500; C04.588.180.390; C17.800.090.500.390

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	decreases expression	5
trichostatin A	affects cotreatment, decreases expression	3
sodium arsenite	decreases expression, increases abundance	2
perfluorooctane sulfonic acid	decreases expression	2
Benzo(a)pyrene	decreases expression, increases methylation	2
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	decreases expression	2
aristolochic acid I	decreases expression	1
FR900359	affects phosphorylation	1
TAK-243	decreases sumoylation	1
dicrotophos	decreases expression	1
geldanamycin	increases expression	1
methylmercuric chloride	decreases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	decreases expression	1
sodium arsenate	decreases expression	1
testosterone undecanoate	affects cotreatment, decreases expression	1
beta-lapachone	increases expression	1
arsenite	affects binding, decreases reaction	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
manganese chloride	increases abundance, increases expression	1
coumarin	affects phosphorylation	1
CGP 52608	affects binding, increases reaction	1
2-palmitoylglycerol	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
bisphenol S	affects cotreatment, decreases expression	1
jinfukang	decreases expression	1
Resveratrol	affects cotreatment, increases expression	1
Vorinostat	decreases expression	1
Acetaminophen	decreases expression	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT03414970	PHASE3	ACTIVE_NOT_RECRUITING	Hypofractionated Radiation Therapy After Mastectomy in Preventing Recurrence in Patients With Stage IIa-IIIa Breast Cancer
NCT00461344	PHASE2	TERMINATED	Docetaxel + Doxorubicin as Neoadjuvant Chemotherapy in Patients With Breast Cancer
NCT07499999	PHASE2	NOT_YET_RECRUITING	Randomized Double-Blind Phase II Trial of Baby Exemestane Versus Baby Tamoxifen in Post-Menopausal Women at High Risk for Breast Cancer
NCT00637364	PHASE1/PHASE2	SUSPENDED	High Intensity Focused Ultrasound Tumor Treatment for Pancreatic Cancer Pain
NCT02779855	PHASE1/PHASE2	COMPLETED	Talimogene Laherparepvec in Combination With Neoadjuvant Chemotherapy in Triple Negative Breast Cancer
NCT01753908	EARLY_PHASE1	COMPLETED	Broccoli Sprout Extract in Treating Patients With Breast Cancer
NCT01796041	EARLY_PHASE1	COMPLETED	Intraoperative Imaging of Breast Cancer With Indocyanine Green
NCT01208974	Not specified	ACTIVE_NOT_RECRUITING	Nipple-Areola Complex (NAC) Irradiation After Nipple-Sparing Mastectomy and Reconstruction
NCT01875198	Not specified	TERMINATED	Oncologic Impact of Splenectomy-omitting Radical Pancreatectomy in Well-selected Left-sided Pancreatic Cancer
NCT03543397	Not specified	UNKNOWN	MRI in Ductal Carcinoma in Situ (DCIS)
NCT03834532	Not specified	COMPLETED	Living Well After Breast Surgery