Table 1 Summary of genes associated with cleft lip with/without cleft palate in humans

ABCA4

ATP binding cassette subfamily A member 4

1p22.1

Nonsyndromic

ABCB1

ATP binding cassette subfamily B member 1

7q21.12

Nonsyndromic

ADAM3A

ADAM metallopeptidase domain 3A

8p11.22

Nonsyndromic

ACSS2

Acyl-coenzyme A synthetase short-chain family member 2

20q11.22

Nonsyndromic

ADAM5

ADAM metallopeptidase domain 5

8p11.22

Nonsyndromic

ADAMTS20

ADAM metallopeptidase with thrombospondin type 1 motif 20

12q12

Nonsyndromic

ADGRL2

Adhesion G protein-coupled receptor L2

1p31.1

Nonsyndromic

ADH1C

Alcohol dehydrogenase 1C (class I), gamma polypeptide

4q23

Nonsyndromic & Syndromic: Fetal alcohol syndrome

AQP7

Aquaporin 7

9p13.3

Nonsyndromic

ARHGAP29

Rho GTPase activating protein 29

1p22.1

Nonsyndromic

ASS1

Argininosuccinate synthase 1

9q34.11

Nonsyndromic

AXIN2

Axin 2

17q24.1

Nonsyndromic

BAG4

BCL2 associated athanogene 4

8p11.23

Nonsyndromic

BCL3

B-cell CLL/lymphoma 3

19q13.32

Nonsyndromic

BHMT2

Betaine-homocysteine S-methyltransferase 2

5q14.1

Nonsyndromic

BLM

Bloom syndrome RecQ like helicase

15q26.1

Nonsyndromic

BMP4

Bone morphogenetic protein 4

14q22.2

Nonsyndromic

BMPR1B

Bone morphogenetic protein receptor type 1B

4q22.3

Nonsyndromic

BRIP1

BRCA1 interacting protein C-terminal helicase 1

17q23.2

Nonsyndromic

CBS

Cystathionine-beta-synthase

21q22.3

Nonsyndromic

CDH1

Cadherin 1

16q22.1

Nonsyndromic

CDH2

Cadherin 2

18q12.1

Nonsyndromic

CENPJ

Centromere protein J

13q12.12-q12.13

Nonsyndromic

CHD7

Chromodomain helicase DNA binding protein 7

8q12.2

Syndromic: CHARGE syndrome

CLPTM1

CLPTM1, transmembrane protein

19q13.32

Nonsyndromic

COL4A2

Collagen type IV alpha 2 chain

13q34

Nonsyndromic

COL4A3

Collagen type IV alpha 3 chain

2q36.3

Nonsyndromic

COL4A4

Collagen type IV alpha 4 chain

2q36.3

Nonsyndromic

COL21A1

Collagen type XXI alpha 1 chain

6p12.1; 6p12.3-p11.2

Nonsyndromic

CR1

Complement C3b/C4b receptor 1 (Knops blood group)

1q32.2

Syndromic: Van der Woude syndrome

CRISPLD2

Cysteine rich secretory protein LCCL domain containing 2

16q24.1

Nonsyndromic

CYP1A1

Cytochrome P450 family 1 subfamily A member 1

15q24.1

Nonsyndromic

CYP2E1

Cytochrome P450 family 2 subfamily E member 1

10q26.3

Nonsyndromic

DCAF7

DDB1 and CUL4 associated factor 7

17q23.3

Nonsyndromic

DHFR

Dihydrofolate reductase

5q14.1

Nonsyndromic

DICER1

Dicer 1, ribonuclease III

14q32.13

Nonsyndromic

DLX1

Distal-less homeobox 1

2q31.1

Nonsyndromic

DMD

Dystrophin

Xp21.2-p21.1

Nonsyndromic

DVL2

Dishevelled segment polarity protein 2

17p13.1

Nonsyndromic

E2F1

E2F transcription factor 1

20q11.22

Nonsyndromic

EFNB1

Ephrin B1

Xq13.1

Syndromic: Craniofrontonasal syndrome

EIF2B3

Eukaryotic translation initiation factor 2B subunit gamma

1p34.1

Nonsyndromic

EGF61

Epidermal growth factor 61

4q25

Nonsyndromic

ESRRG

Estrogen related receptor gamma

1q41

Nonsyndromic

EVC

EvC ciliary complex subunit 1

4p16.2

Nonsyndromic

EVC2

EvC ciliary complex subunit 2

4p16.2

Nonsyndromic

EYA1

EYA transcriptional coactivator and phosphatase 1

8q13.3

Nonsyndromic

F13A1

Coagulation factor XIII A chain

6p25.1

Nonsyndromic

FAM49A

Family with sequence similarity 49 member A

2p24.2

Nonsyndromic

FGF1

Fibroblast growth factor 1

5q31.3

Nonsyndromic

FGF2

Fibroblast growth factor 2

4q28.1

Nonsyndromic

FGF3

Fibroblast growth factor 3

11q13.3

Nonsyndromic

FGF10

Fibroblast growth factor 10

5p12

Nonsyndromic

FGF18

Fibroblast growth factor 18

5q35.1

Nonsyndromic

FGFR1

Fibroblast growth factor receptor 1

8p11.23

Nonsyndromic & Syndromic: Kallmann syndrome

FGFR2

Fibroblast growth factor receptor 2

10q26.13

Nonsyndromic

FOXE1

Forkhead box E1

9q22.33

Nonsyndromic

FOXF2

Forkhead box F2

6p25.3

Nonsyndromic

FOXG1

Forkhead box G1

14q12

Nonsyndromic

FOXP2

Forkhead box protein P2

7q31.1

Nonsyndromic

FZD6

Frizzled class receptor 6

8q22.3

Nonsyndromic

GABRB3

Gamma-aminobutyric acid type A receptor beta 3 subunit

15q12

Nonsyndromic

GAD1

Glutamate decarboxylase 1

2q31.1

Nonsyndromic

GCH1

GTP cyclohydrolase 1

14q22.2

Nonsyndromic

GLI2

GLI family zinc finger 2

2q14.2

Nonsyndromic

GREM1

Gremlin 1, DNA family BMP antagonist

15q13.3

Nonsyndromic

GSTM1

Glutathione S-transferase mu 1

1p13.3

Nonsyndromic

GSTP1

Glutathione S-transferase pi 1

11q13.2

Nonsyndromic

GSTT1

Glutathione S-transferase theta 1

22q11.23

Nonsyndromic

HECTD1

HECT domain E3 Ubiquitin protein ligase 1

14q12

Nonsyndromic

HKDC1

Hexokinase domain containing 1

10q22.1

Nonsyndromic

IRF6

Interferon regulatory factor 6

1q32.2

Nonsyndromic

JAG2

Jagged2

14q32.33

Nonsyndromic

JARID2

Jummonji and AT-rich interaction domain containing 2

6p22.3

Nonsyndromic

KIF2A

Kinesin family member 2A

5q12.1

Nonsyndromic

KIF7

Kinesin family member 7

15q26.1

Nonsyndromic

KISS1R

KISS1 receptor

19p13.3

Syndromic: Kallmann syndrome

KRT18

Keratin 18

12q13.13

Nonsyndromic

LACTB

Lactamase beta

15q22.2

Nonsyndromic

LHX8

LIM homeobox 8

1p31.1

Nonsyndromic

LPHN2

Adhesion G protein-coupled receptor L2

1p31.1

Nonsyndromic

MAFB

MAF bZIP transcription factor B

20q12

Nonsyndromic

MGAM

Maltase-glucoamylase

7q34

Nonsyndromic

MID1

Midline 1

Xp22.2

Nonsyndromic & Syndromic: Opitz G/BBB syndrome

MMP3

Matrix metallopeptidase 3

11q22.2

Nonsyndromic

MMP9

Matrix metallopeptidase 9

20q13.12

Nonsyndromic

MROH7

Maestro heat like repeat family member 7

1p32.3

Nonsyndromic

MRPL53

Mitochondrial ribosomal protein L53

2p13.1

Nonsyndromic

MSX1

msh homeobox 1

4p16.2

Nonsyndromic

MSX2

msh homeobox 2

5q35.2

Nonsyndromic

MTR

5-methyltetrahydrofolate-homocysteine methyltransferase

1q43

Nonsyndromic

MTRR

5-methyltetrahydrofolate-homocysteine methyltransferase reductase

5p15.31

Nonsyndromic

MYH9

Myosin heavy chain 9

22q12.3

Nonsyndromic

MTHFD1

Methylenetetrahydrofolate dehydrogenase, cyclohydrolase and formyltetrahydrofolate synthetase 1

14q23.3

Nonsyndromic

MTHFR

Methylenetetrahydrofolate reductase

1p36.22

Nonsyndromic

NAT1

N-acetyltransferase 1

8p22

Nonsyndromic

NAT2

N-acetyltransferase 2

8p22

Nonsyndromic

NECTIN1

Nectin cell adhesion molecule 1

11q23.3

Nonsyndromic

NECTIN2

Nectin cell adhesion molecule 2

19q13.32

Nonsyndromic

NECTIN3

Nectin cell adhesion molecule 3

3q13.13

Nonsyndromic

NOG

Noggin

17q22

Nonsyndromic

NTN1

Netrin 1

17p13.1

Nonsyndromic

OFC1

Orofacial cleft 1

6p24

Nonsyndromic

OFC2

Orofacial cleft 2

2p14-p13

Nonsyndromic

PAH

Phenylalanine hydroxylase

12q23.2

Nonsyndromic

PARVA

Parvin alpha

11p15.3

Nonsyndromic

PTCH1

Patched 1

9q22.32

Nonsyndromic

PAX3

Paired box 3

2q36.1

Nonsyndromic

PAX7

Paired box 7

1p36.13

Nonsyndromic

PAX9

Paired box 9

14q13.3

Nonsyndromic

PCYT1A

Phosphate cytidylyltransferase 1, choline, alpha

3q29

Nonsyndromic

PDGFC

Platelet derived growth factor C

4q32.1

Nonsyndromic

PEMT

Phosphatidylethanolamine N-methyltransferase

17p11.2

Nonsyndromic

PKP1

Plakophilin 1

1q32.1

Nonsyndromic

PHF8

PHD finger protein 8

Xp11.22

Nonsyndromic

PHYH

Phytanoyl-CoA 2-hydroxylase

10p13

Nonsyndromic

RPS26

Ribosomal Protein S26

12q13.2

Nonsyndromic

PRSS1

Protease, serine 1

7q34

Nonsyndromic

PRSS35

Protease, serine 35

6q14.2

Nonsyndromic

RAD51

RAD51 recombinase

15q15.1

Nonsyndromic

RAD54B

RAD54 homolog B

8q22.1

Nonsyndromic

RARA

Retinoic Acid Receptor Alpha

17q21.2

Nonsyndromic

RECQL5

RecQ like helicase 5

17q25.1

Nonsyndromic

REG3A

Regenerating family member 3 alpha

2p12

Nonsyndromic

REN

Renin

1q32.1

Syndromic: Van der Woude syndrome

RFC1

Replication factor C subunit 1

4p14

Nonsyndromic

RHPN2

Rhophilin Rho GTPase binding protein 2

19q13.11

Nonsyndromic

RUNX2

Runt related transcription factor 2

6p21.1

Nonsyndromic

RYK

Receptor-like tyrosine kinase

3q22.2

Nonsyndromic

SATB2

SATB homeobox 2

2q33.1

Nonsyndromic

SEC16A

SEC 16 homolog A, endoplasmic reticulum export factor

9q34.3

Nonsyndromic

SERPINA6

Serpin family A member 6

14q32.13

Nonsyndromic

SLC6A4

Solute carrier family 6 member 4

17q11.2

Nonsyndromic

SMAD1

SMAD family member 1

4q31.21

Nonsyndromic

SMAD2

SMAD family member 2

18q21.1

Nonsyndromic

SOX9

SRY-box 9

17q24.3

Syndromic: Pierre-Robin Syndrome

SPRY1

Sprouty RTK signaling antagonist 1

4q28.1

Nonsyndromic

SUMO1

Small ubiquitin-like modifier 1

2q33.1

Nonsyndromic

STK32B

Serine/threonine kinase 32B

4p16.2

Nonsyndromic

SYNE3

Spectrin repeat containing nuclear envelop family member 3

14q32.13

Nonsyndromic

TAF1B

TATA-box binding protein associated factor, RNA polymerase I subunit B

2p25.1

Nonsyndromic

TANC2

Tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 2

17q23.2-q23.3

Nonsyndromic

TBX22

T-box 22

Xq21.1

Nonsyndromic

TCN2

Transcobalamin 2

22q12.2

Nonsyndromic

TEX11

Testis expressed 11

Xq13.1

Nonsyndromic

TFAP2A

Transcription factor AP-2 alpha

6p24.3

Nonsyndromic

TGFA

Transforming growth factor alpha

2p13.3

Nonsyndromic

TGFB1

Transforming growth factor beta 1

2p13.3

Nonsyndromic

TGFB2

Transforming growth factor beta 2

1q41

Nonsyndromic

TGFB3

Transforming growth factor beta 3

14q24.3

Nonsyndromic

TIMP2

TIMP metallopeptidase inhibitor 2

17q25.3

Nonsyndromic

TMEM19

transmembrane protein 19

12q21.1

Nonsyndromic

TNS1

Tensin 1

2q35

Nonsyndromic

TOX3

TOX high mobility group box family member 3

16q12.1

Nonsyndromic

TP63

Tumor protein p63

3q28

Syndromic: Hay wells or AEC syndrome

TPH2

Tryptophan hydroxylase 2

12q21.1

Nonsyndromic

TPM1

Tropomyosin 1 (alpha)

15q22.2

Nonsyndromic

TULP4

Tubby like protein 4

6q25.3

Nonsyndromic

TYMS

Thymidylate synthase

18p11.32

Nonsyndromic

VAX1

Ventral anterior homeobox 1

10q25.3

Nonsyndromic

VAX2

Ventral anterior homeobox 2

2p13.3

Nonsyndromic

VWA8

Von Willebrand factor A domain-containing protein 8

13q14.11

Nonsyndromic

WNT3

Wnt family member 3

17q21.31-q21.32

Nonsyndromic

WNT3A

Wnt family member 3A

1q42.13

Nonsyndromic

WNT5A

Wnt family member 5A

3p14.3

Nonsyndromic

WNT5B

Wnt family member 5B

12p13.33

Nonsyndromic

WNT6

Wnt family member 6

2q35

Nonsyndromic

WNT9B

Wnt family member 9B

17q21.32

Nonsyndromic

WNT10A

Wnt family member 10A

2q35

Nonsyndromic

WNT11

Wnt family member 11

11q13.5

Nonsyndromic

YOD1

TOD1 deubiquitinase

1q32.1

Nonsyndromic

ZNF385B

Zinc finger protein 385B

2q31.2-q31.3

Nonsyndromic