KLF13

Summary

KLF13 (KLF transcription factor 13, HGNC:13672) is a protein-coding gene on chromosome 15q13.3, encoding Krueppel-like factor 13 (Q9Y2Y9). Transcription factor that activates expression from GC-rich minimal promoter regions, including genes in the cells of the erythroid lineage.

KLF13 belongs to a family of transcription factors that contain 3 classical zinc finger DNA-binding domains consisting of a zinc atom tetrahedrally coordinated by 2 cysteines and 2 histidines (C2H2 motif). These transcription factors bind to GC-rich sequences and related GT and CACCC boxes (Scohy et al., 2000 [PubMed 11087666]).

Source: NCBI Gene 51621 — RefSeq curated summary.

At a glance

• Gene–disease (curated): congenital heart disease (Moderate, ClinGen)
• GWAS associations: 43
• Clinical variants (ClinVar): 82 total — 5 pathogenic
• Phenotypes (HPO): 18
• Transcription factor: yes — 15 downstream targets (CollecTRI)
• MANE Select transcript: NM_015995

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:13672
Approved symbol	KLF13
Name	KLF transcription factor 13
Location	15q13.3
Locus type	gene with protein product
Status	Approved
Aliases	RFLAT-1, BTEB3, NSLP1, FKLF-2
Ensembl gene	ENSG00000169926
Ensembl biotype	protein_coding
OMIM	605328
Entrez	51621

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 4 protein_coding, 4 protein_coding_CDS_not_defined

ENST00000307145, ENST00000500533, ENST00000558225, ENST00000558673, ENST00000558844, ENST00000558921, ENST00000560473, ENST00000870899

RefSeq mRNA: 1 — MANE Select: NM_015995 NM_015995

CCDS: CCDS10025

Canonical transcript exons

ENST00000307145 — 2 exons

Exon	Start	End
ENSE00001127061	31326835	31327789
ENSE00001325912	31372010	31377899

Expression profiles

Bgee: expression breadth ubiquitous, 169 present calls, max score 98.16.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 48.9897 / max 478.3003, expressed in 1809 samples.

FANTOM5 promoters (18 alternative TSS)

Promoter ID	TPM avg	Samples expressed
145659	26.2292	1796
145663	13.6629	1701
145658	2.9037	1185
145666	0.9982	564
145667	0.9118	545
145665	0.8984	597
145676	0.8685	184
145664	0.5704	240
207452	0.5415	285
145683	0.3798	196

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right hemisphere of cerebellum	UBERON:0014890	98.16	gold quality
cerebellar hemisphere	UBERON:0002245	97.91	gold quality
cerebellar cortex	UBERON:0002129	97.77	gold quality
granulocyte	CL:0000094	97.72	gold quality
right lung	UBERON:0002167	97.67	gold quality
mucosa of transverse colon	UBERON:0004991	96.75	gold quality
right frontal lobe	UBERON:0002810	96.57	gold quality
left lobe of thyroid gland	UBERON:0001120	96.19	gold quality
body of pancreas	UBERON:0001150	96.15	gold quality
leukocyte	CL:0000738	96.10	gold quality
right lobe of thyroid gland	UBERON:0001119	95.97	gold quality
monocyte	CL:0000576	95.91	gold quality
ganglionic eminence	UBERON:0004023	95.85	gold quality
embryo	UBERON:0000922	95.84	gold quality
bone marrow cell	CL:0002092	95.78	gold quality
right coronary artery	UBERON:0001625	95.72	gold quality
anterior cingulate cortex	UBERON:0009835	95.66	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	95.49	gold quality
upper lobe of left lung	UBERON:0008952	95.37	gold quality
Brodmann (1909) area 9	UBERON:0013540	95.35	gold quality
peripheral nervous system	UBERON:0000010	95.29	gold quality
tibial nerve	UBERON:0001323	95.29	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	95.15	gold quality
lower esophagus mucosa	UBERON:0035834	95.14	gold quality
left uterine tube	UBERON:0001303	95.11	gold quality
cerebellum	UBERON:0002037	95.10	gold quality
left coronary artery	UBERON:0001626	94.91	gold quality
small intestine Peyer’s patch	UBERON:0003454	94.89	gold quality
skin of leg	UBERON:0001511	94.88	gold quality
right atrium auricular region	UBERON:0006631	94.84	gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 3.

Experiment	Marker?	Max mean expression
E-HCAD-1	yes	37.57
E-ANND-3	yes	7.19
E-GEOD-137537	yes	5.47
E-GEOD-110499	no	227.85

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

15 targets.

Target	Regulation
CCL5	Unknown
CREBBP
CYP11A1	Repression
CYP1A1	Repression
IL4
KAT2B
KLF13
LDLR	Repression
LHB
NOS2
SMAD7	Repression
STAR	Activation
SUPT7L
TAGLN	Activation
ZNF268

JASPAR motifs

Motif	Name	Family
MA0657.1	KLF13	Three-zinc finger Kruppel-related
MA0657.2	KLF13	Three-zinc finger Kruppel-related

JASPAR matrix evidence (PMIDs): PMID:16266294

Upstream regulators (CollecTRI, top): KLF13, SP1

miRNA regulators (miRDB)

186 targeting KLF13, 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-6748-5P	100.00	65.81	1057
HSA-MIR-7110-3P	100.00	73.18	2486
HSA-MIR-6873-3P	100.00	71.42	2626
HSA-MIR-3162-3P	100.00	65.37	363
HSA-MIR-4455	100.00	65.48	1587
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-19A-3P	99.98	75.33	2762
HSA-MIR-19B-3P	99.98	75.44	2754
HSA-MIR-103A-3P	99.98	69.14	1595
HSA-MIR-107	99.98	69.14	1595
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-9-3P	99.96	70.88	2068
HSA-MIR-302E	99.96	70.74	2669
HSA-MIR-545-3P	99.95	70.74	2783
HSA-MIR-96-5P	99.95	72.80	2140
HSA-MIR-9983-3P	99.94	71.48	3631
HSA-MIR-651-3P	99.94	73.48	5177
HSA-MIR-6721-5P	99.93	68.92	2981
HSA-MIR-1-3P	99.93	72.35	1914
HSA-MIR-206	99.93	72.50	1893
HSA-MIR-338-5P	99.92	72.34	2951
HSA-MIR-12133	99.92	71.82	2006
HSA-MIR-613	99.91	71.50	1710
HSA-MIR-329-3P	99.91	66.56	1234
HSA-MIR-362-3P	99.91	66.38	1267
HSA-MIR-454-3P	99.91	74.01	1925
HSA-MIR-1271-5P	99.91	71.99	1972
HSA-MIR-130A-3P	99.90	73.31	1861
HSA-MIR-130B-3P	99.90	73.27	1850

Literature-anchored findings (GeneRIF, showing 26)

• protein analysis of BTEB3 and BTEB4 and their binding to CYP1A1 (PMID:12036432)
• functional domains and DNA-binding sequences (PMID:12050170)
• A translational rheostat for RFLAT-1 regulates RANTES expression in T lymphocytes. (PMID:12093895)
• Feedback mechanism for the transcriptional control of the KLF13 gene in the erythroid environment. (PMID:15716005)
• In co-transfection assays in K562 cells, it was demonstrated that KLF2, 5 and 13 positively regulate, and KLF8 negatively regulates, the gamma-globin gene through the CACCC promoter element. (PMID:16023392)
• KLF13 is a key regulator of late RANTES expression in T lymphocytes (PMID:17074812)
• Coexpression of PRP4 and KLF13 increases nuclear localization of KLF13 and CCL5 transcription. (PMID:17513757)
• Transient transfection of Kruppel-like factor 4 suppressed LDLR, steroidogenic acute regulatory protein, and CYP11A (PMID:18056793)
• Data support cross-regulation among BMP2, KLF9, and KLF13 to maintain progesterone sensitivity in stromal cells undergoing differentiation and suggest that loss of this network compromises establishment of uterine receptivity and implantation success. (PMID:20410205)
• No associations were found between maternal genetic polymorphisms in RANTES (-403G/A) and mother-to-child HIV-1 transmission; plasma, cervical and breastmilk viral loads; or breastmilk chemokine concentrations. (PMID:20518834)
• KLF13 contributes to malignancy in oral cancer cells and may be a useful biomarker fo early detection and da possible target for therapy. (PMID:20539070)
• Knockdown of either FBW7gamma or GSK3beta by small interfering RNA increases KLF13 expression in resting human T lymphocytes. (PMID:22797700)
• KLF13 is critical for the activation of the HPV productive life cycle and is likely involved in initiation and progression of cervical cancer. (PMID:27041562)
• Our results suggest the cg07814318 site could be involved in orexigenic processes, and also implicate KLF13 in obesity. Our findings are the first to associate methylation levels in blood with brain activity in obesity-related regions, and further support previous findings between ghrelin, brain activity and genetic differences. (PMID:28194012)
• Results show that cg07814318 methylation in blood was significantly associated with obesity and correlated with several obesity-related physical and biochemical traits. The exome sequencing of KLF13 gene in blood identified nine SNPs within its gene body, and two SNPs as cis-meQTL of cg07814318. The sequencing variations within KLF13 genes could drive dynamic modifications of obesity-related CpG methylation. (PMID:28508896)
• SLC44A1 and KLF13 may be involved in tumorigenesis and the metastasis of colon cancer by miRNA regulation (PMID:29408621)
• KLF13 functions as a tumor suppressor protein in PCa, and the pharmacological activation of KLF13 might represent a potential approach for the treatment of prostate cancer. (PMID:29843216)
• Our results show that the S156N and P163S variants may affect the transcriptional function of KLF13 and physical interaction with TBX5. These results identified KLF13 as a potential genetic risk factor for congenital heart disease. (PMID:32293321)
• Molecular Mechanisms for Kruppel-Like Factor 13 Actions in Hippocampal Neurons. (PMID:32578009)
• KLF13 loss-of-function variation contributes to familial congenital heart defects. (PMID:33215447)
• The inhibitory effect of LINC00261 upregulation on the pancreatic cancer EMT process is mediated by KLF13 via the mTOR signaling pathway. (PMID:35066757)
• KLF13 Loss-of-Function Mutations Underlying Familial Dilated Cardiomyopathy. (PMID:36346048)
• UC-BSCs Exosomes Regulate Th17/Treg Balance in Patients with Systemic Lupus Erythematosus via miR-19b/KLF13. (PMID:36552891)
• Kruppel-like Factors 3 Regulates Migration and Invasion of Gastric Cancer Cells Through NF-kappaB Pathway. (PMID:36580668)
• Kruppel-like factor 13 acts as a tumor suppressor in thyroid carcinoma by downregulating IFIT1. (PMID:37817224)
• KLF13 restrains Dll4-muscular Notch2 axis to improve the muscle atrophy. (PMID:38973459)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
mus_musculus	Klf13	ENSMUSG00000052040
rattus_norvegicus	Klf13	ENSRNOG00000015822
drosophila_melanogaster	luna	FBGN0040765

Paralogs (22): KLF6 (ENSG00000067082), KLF8 (ENSG00000102349), KLF5 (ENSG00000102554), KLF1 (ENSG00000105610), KLF3 (ENSG00000109787), KLF7 (ENSG00000118263), KLF12 (ENSG00000118922), KLF9 (ENSG00000119138), KLF2 (ENSG00000127528), KLF16 (ENSG00000129911), KLF4 (ENSG00000136826), KLF10 (ENSG00000155090), KLF15 (ENSG00000163884), SP8 (ENSG00000164651), SP7 (ENSG00000170374), KLF17 (ENSG00000171872), KLF11 (ENSG00000172059), SP6 (ENSG00000189120), SP5 (ENSG00000204335), SP9 (ENSG00000217236), KLF14 (ENSG00000266265), KLF18 (ENSG00000283039)

Protein

Protein identifiers

Krueppel-like factor 13 — Q9Y2Y9 (reviewed: Q9Y2Y9)

Alternative names: Basic transcription element-binding protein 3, Novel Sp1-like zinc finger transcription factor 1, RANTES factor of late activated T-lymphocytes 1, Transcription factor BTEB3, Transcription factor NSLP1

All UniProt accessions (4): Q9Y2Y9, H0YK05, H0YKM8, X5DNR2

UniProt curated annotations — full annotation on UniProt →

Function. Transcription factor that activates expression from GC-rich minimal promoter regions, including genes in the cells of the erythroid lineage. Represses transcription by binding to the BTE site, a GC-rich DNA element, in competition with the activator SP1. It also represses transcription by interacting with the corepressor Sin3A and HDAC1. Activates RANTES and CCL5 expression in T-cells.

Subcellular location. Nucleus.

Tissue specificity. Ubiquitous.

Post-translational modifications. Phosphorylated by PRP4K; phosphorylation regulates its transcriptional modulator activity.

Domain organisation. The Ala/Pro-rich domain may contain discrete activation and repression subdomains and also can mediate protein-protein interactions.

Similarity. Belongs to the Sp1 C2H2-type zinc-finger protein family.

RefSeq proteins (1): NP_057079* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR013087	Znf_C2H2_type	Domain
IPR036236	Znf_C2H2_sf	Homologous_superfamily

Pfam: PF00096

UniProt features (19 total): compositionally biased region 5, modified residue 5, zinc finger region 3, region of interest 3, sequence conflict 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9Y2Y9-F1	58.91	0.00

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 (5): 268, 270, 279, 283, 287

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-9976102	Differentiation of naive CD4+ T cells to T helper 2 cells (Th2 cells)

MSigDB gene sets: 328 (showing top): GOBP_MYELOID_CELL_DIFFERENTIATION, GOBP_MYELOID_CELL_HOMEOSTASIS, PAX4_01, LU_IL4_SIGNALING, GCANCTGNY_MYOD_Q6, GOBP_ERYTHROCYTE_HOMEOSTASIS, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, chr15q13, DARWICHE_SKIN_TUMOR_PROMOTER_UP, DARWICHE_PAPILLOMA_RISK_LOW_DN, AP4_Q6, DARWICHE_PAPILLOMA_RISK_HIGH_UP, CREBP1_Q2, DARWICHE_SQUAMOUS_CELL_CARCINOMA_UP, CTATGCA_MIR153

GO Biological Process (5): regulation of transcription by RNA polymerase II (GO:0006357), transcription by RNA polymerase II (GO:0006366), negative regulation of cell population proliferation (GO:0008285), negative regulation of erythrocyte differentiation (GO:0045647), positive regulation of transcription by RNA polymerase II (GO:0045944)

GO Molecular Function (8): RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978), DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), DNA-binding transcription activator activity, RNA polymerase II-specific (GO:0001228), zinc ion binding (GO:0008270), sequence-specific double-stranded DNA binding (GO:1990837), DNA binding (GO:0003677), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (2): chromatin (GO:0000785), nucleus (GO:0005634)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
Differentiation of T cells	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
RNA polymerase II transcription regulatory region sequence-specific DNA binding	3
transcription by RNA polymerase II	2
regulation of transcription by RNA polymerase II	2
regulation of DNA-templated transcription	1
DNA-templated transcription	1
cell population proliferation	1
regulation of cell population proliferation	1
negative regulation of cellular process	1
erythrocyte differentiation	1
negative regulation of myeloid cell differentiation	1
regulation of erythrocyte differentiation	1
positive regulation of DNA-templated transcription	1
cis-regulatory region sequence-specific DNA binding	1
chromatin	1
DNA-binding transcription factor activity	1
DNA-binding transcription factor activity, RNA polymerase II-specific	1
DNA-binding transcription activator activity	1
positive regulation of transcription by RNA polymerase II	1
transition metal ion binding	1
double-stranded DNA binding	1
sequence-specific DNA binding	1
nucleic acid binding	1
binding	1
cation binding	1
chromosome	1
cellular anatomical structure	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

976 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
KLF13	MTMR10	Q9NXD2	705
KLF13	OTUD7A	Q8TE49	647
KLF13	SIN3A	Q96ST3	630
KLF13	GYPB	P06028	624
KLF13	ALAS2	P22557	615
KLF13	HBE1	P02100	598
KLF13	ALAS1	P13196	590
KLF13	CCL5	P13501	590
KLF13	FECH	P22830	571
KLF13	HMBS	P08396	558
KLF13	TRPM1	Q7Z4N2	556
KLF13	FAN1	Q9Y2M0	524
KLF13	GATA1	P15976	523
KLF13	PRP4K	Q13523	523
KLF13	GATA4	P43694	517

IntAct

15 interactions, top by confidence:

A	B	Type	Score
PRP4K	KLF13	psi-mi:“MI:0915”(physical association)	0.640
KLF13	PRP4K	psi-mi:“MI:0915”(physical association)	0.640
KLF13	PRP4K	psi-mi:“MI:0217”(phosphorylation reaction)	0.640
PRP4K	KLF13	psi-mi:“MI:0403”(colocalization)	0.640
CHCHD10	CLPX	psi-mi:“MI:0914”(association)	0.640
GATA4	KLF13	psi-mi:“MI:0915”(physical association)	0.520
KLF13	GATA4	psi-mi:“MI:0915”(physical association)	0.520
	KLF13	psi-mi:“MI:0407”(direct interaction)	0.440
KLF13	GATA6	psi-mi:“MI:0915”(physical association)	0.400
PCBD1	KLF13	psi-mi:“MI:0915”(physical association)	0.370
Srsf1	SRRM1	psi-mi:“MI:0914”(association)	0.350
CHCHD10	ZNF593	psi-mi:“MI:0914”(association)	0.350
CHCHD2	ZNF593	psi-mi:“MI:0914”(association)	0.350

BioGRID (28): KLF13 (Affinity Capture-MS), KLF13 (Affinity Capture-MS), KLF13 (Affinity Capture-RNA), SIN3A (Reconstituted Complex), KLF13 (Affinity Capture-MS), CREBBP (Phenotypic Enhancement), CREBBP (Affinity Capture-Western), KLF13 (Affinity Capture-Western), KLF13 (Affinity Capture-Western), SERPINH1 (Affinity Capture-Western), KAT2B (Affinity Capture-Western), KLF13 (Affinity Capture-Western), KLF13 (Reconstituted Complex), KLF13 (Biochemical Activity), KLF13 (Biochemical Activity)

ESM2 similar proteins: A0A286YF58, A0A494C0N9, A0A494C0Y3, A0A7I2V3R4, A2VDX9, A6NIN4, D3YXK1, G3UXB3, O15370, O15522, O35392, O70218, O70220, O89113, P0DPE3, P12980, P17542, P22091, P28283, P82976, Q04890, Q05916, Q05917, Q13461, Q14V87, Q15270, Q19A40, Q5T230, Q5VY09, Q63244, Q6F5E0, Q6SPE9, Q6SPF0, Q7RTU7, Q80WY3, Q8TD94, Q8WY41, Q8WZ71, Q91XV7, Q96Q04

Diamond homologs: A1C6L9, A1DH89, A2QCJ9, B0XSK6, B8NGC8, G4N3L5, K9GKQ6, O14335, O74252, O94166, P08047, P0CG40, P10069, P13574, P27705, P43079, P46099, P58334, P78871, Q01981, Q05620, Q08400, Q0VA40, Q13351, Q14V87, Q19A40, Q22678, Q24266, Q3SY56, Q4WRE4, Q4X0Z3, Q5AMH6, Q5XGT8, Q62511, Q64HY3, Q64HY5, Q6BEB4, Q6NW96, Q6P0J3, Q8BMJ8

SIGNOR signaling

6 interactions.

A	Effect	B	Mechanism
PRPF4B	down-regulates	KLF13	phosphorylation
MAPK9	“down-regulates quantity by destabilization”	KLF13	phosphorylation
KLF13	“up-regulates activity”	SIN3A	binding

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	5
Likely pathogenic	0
Uncertain significance	60
Likely benign	9
Benign	2

Top pathogenic / likely-pathogenic (5)

Variant ID	HGVS	Classification
146727	GRCh38/hg38 15q13.2-13.3(chr15:30361656-32150923)x3	Pathogenic
446332	GRCh37/hg19 15q13.2-13.3(chr15:31140606-32438944)x1	Pathogenic
625712	GRCh37/hg19 15q11.2-13.3(chr15:22382860-32396457)	Pathogenic
625834	GRCh37/hg19 15q13.2-13.3(chr15:30927362-32404084)	Pathogenic
997068	GRCh37/hg19 15q13.2-13.3(chr15:30943903-32510863)	Pathogenic

SpliceAI

871 predictions. Top by Δscore:

Variant	Effect	Δscore
15:31372004:CCACA:C	acceptor_loss	1.0000
15:31372005:CACA:C	acceptor_loss	1.0000
15:31372008:A:C	acceptor_loss	1.0000
15:31372009:G:T	acceptor_loss	1.0000
15:31372009:GGT:G	acceptor_gain	1.0000
15:31372009:GGTGA:G	acceptor_gain	1.0000
15:31358919:A:T	donor_gain	0.9900
15:31358972:G:T	donor_gain	0.9900
15:31372008:A:AG	acceptor_gain	0.9900
15:31372008:AG:A	acceptor_gain	0.9900
15:31372008:AGGT:A	acceptor_gain	0.9900
15:31372009:G:GG	acceptor_gain	0.9900
15:31372009:GG:G	acceptor_gain	0.9900
15:31372009:GGTG:G	acceptor_gain	0.9900
15:31346774:G:GA	donor_gain	0.9800
15:31372001:T:TA	acceptor_gain	0.9800
15:31327788:AGGTC:A	donor_loss	0.9700
15:31327789:GGT:G	donor_loss	0.9700
15:31327790:G:A	donor_loss	0.9700
15:31327791:T:A	donor_loss	0.9700
15:31358893:G:T	donor_gain	0.9700
15:31372337:G:GG	donor_gain	0.9700
15:31346755:G:T	donor_gain	0.9600
15:31358918:G:GT	donor_gain	0.9600
15:31327707:G:GT	donor_gain	0.9500
15:31358972:G:GT	donor_gain	0.9500
15:31346766:C:T	donor_gain	0.9300
15:31358860:G:GT	donor_gain	0.9300
15:31372006:ACAG:A	acceptor_gain	0.9300
15:31337402:G:T	donor_gain	0.9200

AlphaMissense

1861 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
15:31327732:T:A	C174S	1.000
15:31327733:G:C	C174S	1.000
15:31327783:C:G	H191D	1.000
15:31327785:C:A	H191Q	1.000
15:31327785:C:G	H191Q	1.000
15:31372021:T:C	F197L	1.000
15:31372023:C:A	F197L	1.000
15:31372023:C:G	F197L	1.000
15:31372027:T:C	C199R	1.000
15:31372043:G:A	C204Y	1.000
15:31372054:T:C	F208L	1.000
15:31372055:T:C	F208S	1.000
15:31372055:T:G	F208C	1.000
15:31372056:C:A	F208L	1.000
15:31372056:C:G	F208L	1.000
15:31372081:C:G	H217D	1.000
15:31372083:C:A	H217Q	1.000
15:31372083:C:G	H217Q	1.000
15:31372093:C:G	H221D	1.000
15:31372095:C:A	H221Q	1.000
15:31372095:C:G	H221Q	1.000
15:31372111:T:C	F227L	1.000
15:31372113:C:A	F227L	1.000
15:31372113:C:G	F227L	1.000
15:31372117:T:C	C229R	1.000
15:31372126:T:A	C232S	1.000
15:31372126:T:C	C232R	1.000
15:31372127:G:A	C232Y	1.000
15:31372127:G:C	C232S	1.000
15:31372128:C:G	C232W	1.000

dbSNP variants (sampled 300 via entrez): RS1000023945 (15:31399542 A>G), RS1000063088 (15:31355646 G>A), RS1000076300 (15:31399308 A>T), RS1000078509 (15:31353167 T>C), RS1000086185 (15:31361271 G>C), RS1000099843 (15:31326212 G>A,C), RS1000110514 (15:31388234 T>C), RS1000145304 (15:31340911 G>A), RS1000169886 (15:31384174 C>T), RS1000176052 (15:31414038 A>C), RS1000198254 (15:31376541 A>G), RS1000239329 (15:31346030 C>G), RS1000256422 (15:31399255 C>G,T), RS1000278061 (15:31420479 T>C,G), RS1000283506 (15:31413201 AAC>A)

Disease associations

OMIM: gene MIM:605328 | disease phenotypes: MIM:608636

GenCC curated gene-disease

Disease	Classification	Inheritance
congenital heart disease	Moderate	Autosomal dominant

ClinGen Gene-Disease Validity (1)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

Disease	Classification	Inheritance
congenital heart disease	Moderate	AD

Mondo (2): congenital heart disease (MONDO:0005453), 15q11q13 microduplication syndrome (MONDO:0012081)

Orphanet (1): 15q11q13 microduplication syndrome (Orphanet:238446)

HPO phenotypes

18 total (18 of 18 shown, HPO-id order):

HPO	Term
HP:0000006	Autosomal dominant inheritance
HP:0000316	Hypertelorism
HP:0000377	Abnormal pinna morphology
HP:0000486	Strabismus
HP:0000664	Synophrys
HP:0000708	Atypical behavior
HP:0001156	Brachydactyly
HP:0001250	Seizure
HP:0001252	Hypotonia
HP:0001256	Mild intellectual disability
HP:0001328	Specific learning disability
HP:0001999	Abnormal facial shape
HP:0002342	Moderate intellectual disability
HP:0003829	Typified by incomplete penetrance
HP:0004209	Clinodactyly of the 5th finger
HP:0008050	Abnormality of the palpebral fissures
HP:0010864	Severe intellectual disability
HP:0030680	Abnormal cardiovascular system morphology

GWAS associations

43 associations (top):

Study	Trait	p-value
GCST002527_10	Eosinophilic esophagitis	6.000000e-10
GCST002782_119	Waist-to-hip ratio adjusted for body mass index	1.000000e-06
GCST002782_120	Waist-to-hip ratio adjusted for body mass index	1.000000e-09
GCST002782_121	Waist-to-hip ratio adjusted for body mass index	3.000000e-07
GCST002782_122	Waist-to-hip ratio adjusted for body mass index	1.000000e-10
GCST004346_58	Psoriasis	9.000000e-10
GCST004505_68	Waist-to-hip ratio adjusted for BMI (adjusted for smoking behaviour)	1.000000e-07
GCST004505_69	Waist-to-hip ratio adjusted for BMI (adjusted for smoking behaviour)	2.000000e-09
GCST004507_19	Waist-to-hip ratio adjusted for BMI (joint analysis main effects and smoking interaction)	7.000000e-06
GCST004508_13	Waist-to-hip ratio adjusted for BMI in non-smokers	8.000000e-06
GCST004567_119	Waist-to-hip ratio adjusted for BMI (joint analysis for main effect and physical activity interaction)	9.000000e-08
GCST004576_25	Waist-to-hip ratio adjusted for body mass index	3.000000e-08
GCST004578_45	Waist-to-hip ratio adjusted for BMI in active individuals	1.000000e-06
GCST004794_1	Brain volume in infants (intracranial brain volume)	1.000000e-07
GCST005993_58	Mean corpuscular hemoglobin	1.000000e-09
GCST006011_32	Mean corpuscular volume	2.000000e-12
GCST010242_259	HDL cholesterol levels	1.000000e-09
GCST010244_174	Triglyceride levels	2.000000e-08
GCST010727_32	Deep white matter hyperintensities	5.000000e-06
GCST012227_282	Hip circumference adjusted for BMI	2.000000e-08
GCST012228_494	Waist-hip index	3.000000e-08
GCST012228_495	Waist-hip index	1.000000e-09
GCST012228_496	Waist-hip index	1.000000e-08
GCST012229_214	Hip index	1.000000e-10
GCST012229_215	Hip index	2.000000e-10
GCST012229_216	Hip index	2.000000e-14
GCST012230_138	Waist-to-hip ratio adjusted for BMI	3.000000e-09
GCST012230_139	Waist-to-hip ratio adjusted for BMI	4.000000e-08
GCST90000025_204	Appendicular lean mass	2.000000e-13
GCST90002385_41	High light scatter reticulocyte count	4.000000e-12

EFO canonical traits (11, from GWAS)

EFO ID	Trait name
EFO:0007788	BMI-adjusted waist-hip ratio
EFO:0004318	smoking behavior
EFO:0008002	physical activity measurement
EFO:0008369	infant intracranial volume measurement
EFO:0004527	mean corpuscular hemoglobin
EFO:0004612	high density lipoprotein cholesterol measurement
EFO:0004530	triglyceride measurement
EFO:0005665	white matter hyperintensity measurement
EFO:0008039	BMI-adjusted hip circumference
EFO:0004980	appendicular lean mass
EFO:0007986	reticulocyte count

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D006330	Heart Defects, Congenital	C14.240.400; C14.280.400; C16.131.240.400

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Benzene	increases expression	2
Benzo(a)pyrene	affects methylation, decreases methylation, increases methylation	2
Estradiol	increases expression	2
Tretinoin	decreases expression, increases expression	2
Valproic Acid	affects expression, 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	increases phosphorylation	1
dicrotophos	increases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	decreases methylation	1
geraniol	increases expression	1
sodium arsenite	decreases expression	1
cobaltous chloride	decreases expression	1
benzo(e)pyrene	increases methylation	1
aflatoxin B2	increases methylation	1
beta-methylcholine	affects expression	1
CGP 52608	affects binding, increases reaction	1
erucylphospho-N,N,N-trimethylpropylammonium	increases expression	1
ICG 001	increases expression	1
abrine	decreases expression	1
jinfukang	increases expression	1
PCI 5002	affects cotreatment, increases expression	1
Arsenic Trioxide	decreases expression	1
Acetaminophen	decreases expression	1
Arsenic	affects methylation	1
Doxorubicin	decreases expression	1
Methapyrilene	increases methylation	1
Methyl Methanesulfonate	decreases expression	1
Silicon Dioxide	decreases expression	1

Cellosaurus cell lines

2 cell lines: 1 cancer cell line, 1 transformed cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_AW33	K562 eGFP-KLF13	Cancer cell line	Female
CVCL_XV68	HEK293 eGFP-KLF13	Transformed cell line	Female

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT00668824	PHASE4	UNKNOWN	Improved Diagnosis of Congenital Heart Disease by Magnetic Resonance Imaging Using Vasovist
NCT01368705	PHASE4	COMPLETED	Nitrogen Balance in Infants After Post Cardiothoracic Surgery
NCT01619982	PHASE4	COMPLETED	Pre-operative Prophylaxis With Vancomycin and Cefazolin in Pediatric Cardiovascular Surgery Patients
NCT02122679	PHASE4	WITHDRAWN	Tranexamic Acid Effect on Platelet Aggregation Following Infant Cardiopulmonary Bypass
NCT02527811	PHASE4	UNKNOWN	Ulinastatin Injection in in Pediatric Patients Undergoing Open Heart Surgery
NCT03014700	PHASE4	COMPLETED	Fibrinogen Concentrate vs Cryoprecipitate
NCT03408340	PHASE4	TERMINATED	Paravertebral Nerve Blocks in Neonates
NCT03630796	PHASE4	UNKNOWN	Effect of Sevoflurane in Postoperative Troponin I Levels in Children Undergoing Congenital Heart Defects Surgery
NCT03667703	PHASE4	COMPLETED	Stress Ulcer Prophylaxis Versus Placebo in Critically Ill Infants With Congenital Heart Disease
NCT04453761	PHASE4	UNKNOWN	Thiamine Influenced on Substrate Energy Effectiveness in Indonesian Children Undergoing Cardiopulmonary Bypass
NCT06668389	PHASE4	RECRUITING	Sodium-Glucose Cotransporter 2 Inhibitors for Repaired Tetralogy of Fallot Patients for Enhancement of Cardio-Pulmonary Status Trial
NCT07499154	PHASE4	NOT_YET_RECRUITING	Perioperative Lidocaine for Lung Protection in Infants Undergoing Cardiac Surgery
NCT00000470	PHASE3	COMPLETED	Infant Heart Surgery: Central Nervous System Sequelae of Circulatory Arrest
NCT00000494	PHASE3	COMPLETED	Management of Patent Ductus in Premature Infants
NCT01134302	PHASE3	UNKNOWN	Hybrid Versus Norwood Management Strategies in Infants Undergoing Single Ventricle Palliation
NCT01607983	PHASE3	WITHDRAWN	Effects of Pulmonary Vasodilation Upon VA Coupling in Fontan Patients
NCT01662011	PHASE3	UNKNOWN	Application of Neurally Adjusted Ventilatory Assist to Children After Congenital Cardiac Surgery
NCT02320669	PHASE3	COMPLETED	Phase 3 Triiodothyronine Supplementation for Infants After Cardiopulmonary Bypass
NCT02615262	PHASE3	COMPLETED	Intraoperative Dexamethasone in Pediatric Cardiac Surgery
NCT03153137	PHASE3	COMPLETED	Clinical Study Assessing the Efficacy and Safety of Macitentan in Fontan-palliated Subjects
NCT03154476	PHASE3	COMPLETED	Role of Sildenafil for Fontan Associated Liver Disease (SiFALD) Study
NCT04536194	PHASE3	COMPLETED	Dopamine Versus Norepinephrine Under General Anesthesia
NCT04702373	PHASE3	ACTIVE_NOT_RECRUITING	Training in Exercise Activities and Motion for Growth (TEAM 4 Growth) RCT
NCT05049590	PHASE3	COMPLETED	Acute Normovolemic Hemodilution in Complex Cardiac Surgery
NCT06406517	PHASE3	UNKNOWN	Comparative Effectiveness of Gadopiclenol for Evaluation of Adult Congenital Heart Anatomy and Hemodynamics
NCT06693674	PHASE3	RECRUITING	Effect of Sacubitril-Valsartan on Cardiac Structure and Function
NCT06955260	PHASE3	NOT_YET_RECRUITING	SGLT2 Inhibition With Empagliflozin in Fontan Circulatory Failure
NCT00115375	PHASE2	COMPLETED	Platelet Aggregation Inhibition in Children on Clopidogrel (PICOLO)
NCT00350220	PHASE2	COMPLETED	Transfusion Strategies in Pediatric Cardiothoracic Surgery
NCT00374088	PHASE2	COMPLETED	N-Acetylcysteine in Neonatal Congenital Heart Surgery (INACT Study)
NCT00538785	PHASE2	COMPLETED	A Study to Evaluate MEDI-524 In Children With Hemodynamically Significant Congenital Heart Disease
NCT00770705	PHASE2	WITHDRAWN	Parenteral Phenoxybenzamine During Congenital Heart Disease Surgery
NCT00919945	PHASE2	TERMINATED	Impact of Early Enteral Feeding on Splanchnic Blood Flow After Surgery for Critical Heart Disease in the Newborn
NCT01063712	PHASE2	COMPLETED	Safety and Effectiveness of the Device Nit-Occlud® PDA-R
NCT01069510	PHASE2	COMPLETED	Spironolactone in Adult Congenital Heart Disease
NCT01189981	PHASE2	COMPLETED	Effect of eHealth Encouragements to Intensive Exercise in Adolescents With Congenital Heart Disease
NCT01330433	PHASE2	COMPLETED	Effects of CoSeal on Bleeding & Adhesions in Pediatric Heart Surgery
NCT01662037	PHASE2	COMPLETED	Bosentan Therapy in Children With Functional Single Ventricle
NCT01668264	PHASE2	UNKNOWN	Imaging Assessment of Diastolic Function
NCT01827059	PHASE2	UNKNOWN	Bosentan In Exercise Induced Pulmonary Arterial Hypertension in CongenitaL Heart diseasE