Genes associated with “macrocephaly”

Diagnostic yield calculator →
761 genes foundHPO: MacrocephalyOpen Targets: Macrocephaly
How are genes scored? (0–100 composite)
-5–15
ClinGen
0–15
HPO Freq
0–15
Open Targets
0–12
Phen2Gene
0–10
ClinVar
0–8
Constraint
0–8
Dosage
0–8
OMIM CS
0–8
PanelApp
0–5
OMIM
0–5
G2P
0–4
Breadth
Tiers:Strong Candidates (≥20)Consider (≥8)Possible (≥3)
Evidence dots:
HPOClinVarPhen2GeneOpen TargetsPanelApp
hover for details

Strong Candidates

20 genes
1
CHD8 →

chromodomain helicase DNA binding protein 8

38
score
ClinGen: DefinitiveGTR ↑

Macrocephaly

Frequency
72%
n=46
P/LP Variants
26
OT Score
0.41
2
PTEN →

phosphatase and tensin homolog

38
score
ClinGen: DefinitiveACMG SFP2G #2GTR ↑

Postnatal macrocephaly

Frequency
100%
n=3
P/LP Variants
64
OT Score
0.56
3
36
score
ClinGen: DefinitiveP2G #3GTR ↑

Macrocephaly

Frequency
58%
n=48
P/LP Variants
7
OT Score
-
4
35
score
ClinGen: DefinitiveGTR ↑

Macrocephaly

Frequency
88%
n=131
P/LP Variants
15
OT Score
-
5
CHD3 →

chromodomain helicase DNA binding protein 3

33
score
ClinGen: DefinitiveGTR ↑

Macrocephaly

Frequency
61%
n=31
P/LP Variants
5
OT Score
0.37
6
NFIB →

nuclear factor I B

32
score
ClinGen: DefinitiveGTR ↑

Macrocephaly

Frequency
81%
n=16
P/LP Variants
5
OT Score
0.53
7
MTOR →

mechanistic target of rapamycin kinase

32
score
ClinGen: DefinitiveGTR ↑

Macrocephaly

Frequency
100%
n=4
P/LP Variants
4
OT Score
0.29
8
PTCH1 →

patched 1

31
score
ClinGen: DefinitiveP2G #9GTR ↑

Macrocephaly

Frequency
-
P/LP Variants
15
OT Score
0.33
9
NSD1 →

nuclear receptor binding SET domain protein 1

30
score
ClinGen: DefinitiveP2G #7GTR ↑
Frequency
-
P/LP Variants
16
OT Score
0.27
30NF1
Def

Macrocephaly

29FGFR3
Def#1

Macrocephaly

28EZH2
Def#5

Macrocephaly

27PIK3CA
Ref#13

Progressive macrocephaly

27KIF7
#4

Macrocephaly

27NFIA
Def

Macrocephaly

26BRWD3
Def

bromodomain and WD repeat domain containing 3

25SPRED1
Def

Macrocephaly

23ASPA
Def#12

Macrocephaly

22GPC3
Def#17

Macrocephaly

21MLC1
Def

Macrocephaly

Consider

97 genes
20ZBTB20
Def

Macrocephaly

19KPTN
Def

Macrocephaly

19NFIX
Def
18DNMT3A
Def

Macrocephaly

18HEPACAM
Def

Macrocephaly

17INPPL1
Def
17TCIRG1
Def
17MED12
Def
16SETD2
Def

Postnatal macrocephaly

15KMT2E
Def

Macrocephaly

15DICER1
Def
15TRIP12
Def
15AKT3
Def

AKT serine/threonine kinase 3

14WNT5A
Mod
14WDFY3
Def

WD repeat and FYVE domain containing 3

14AMER1
Def

Macrocephaly

13KRAS
Def#6

Relative macrocephaly

13ABCC9
Def

ATP binding cassette subfamily C member 9

13AGA
Def
13COMMAD

COLOBOMA, OSTEOPETROSIS, MICROPHTHALMIA, MACROCEPHALY, ALBINISM, AND DEAFNESS; COMMAD

13CORO1A
Def
13IDDAM

INTELLECTUAL DEVELOPMENTAL DISORDER WITH AUTISM AND MACROCEPHALY; IDDAM

13IDDMSSD

INTELLECTUAL DEVELOPMENTAL DISORDER WITH MACROCEPHALY, SEIZURES, AND SPEECH DELAY; IDDMSSD

13MACID

MACROCEPHALY, ACQUIRED, WITH IMPAIRED INTELLECTUAL DEVELOPMENT; MACID

13MDFPMR

MACROCEPHALY, DYSMORPHIC FACIES, AND PSYCHOMOTOR RETARDATION; MDFPMR

13MNDLFH

MACROCEPHALY, NEURODEVELOPMENTAL DELAY, LYMPHOID HYPERPLASIA, AND PERSISTENT FETAL HEMOGLOBIN; MNDLFH

13MRD63

INTELLECTUAL DEVELOPMENTAL DISORDER, AUTOSOMAL DOMINANT 63, WITH MACROCEPHALY; MRD63

13PRRT2
Def
13TET3
Def
13TRIO
Def
12MAPK3
12AKT1
Lim#8

Macrocephaly

12L1CAM
Def
11CUL7

Relative macrocephaly

11BRAF
Def

Macrocephaly

11PTPN11
Def

Macrocephaly

11CACNA1E
Def

Macrocephaly

10HMGA2
Def

Relative macrocephaly

10RIT1
Def

Relative macrocephaly

10SOX9
Def

Macrocephaly

10MAP2K1
Def#20

Macrocephaly

10STXBP1
Def

syntaxin binding protein 1

10RPS6KA3
Def

ribosomal protein S6 kinase A3

10SATB2
Def

SATB homeobox 2

10ALDOA
10ASPHD1
10C16ORF54
10CDIPT
10CDIPTOSP
10DOC2A
10FIMP1
10GDPD3
10HIRIP3
10INO80E
10KCTD13
10KCTD13-DT
10KIF22
10MVP-DT
10OBSL1
10PAGR1
10PPP4C
10SEZ6L2
10SPATA22
10TAOK2
10TBX6
10TLCD3B
10TMEM219
10YPEL3
10YPEL3-DT
10ZG16
10ERF
Def

ETS2 repressor factor

10HERC1

Macrocephaly

10GNS
Def

Macrocephaly

10IFT80
Def
9CHD4
Def
9FAM111A
Def
9ARSB
Def

Macrocephaly

9ODC1

Macrocephaly

9ARID1B
Def
9ARID2
Def
9COL2A1
Def
9KMT2D
Def
9MITF
Def
9TBL1XR1
Def
9FBN1
DefSF

fibrillin 1

9GNAI3
Mod

Macrocephaly

9FAM177A1

Macrocephaly

9PPP1CB
Def

Macrocephaly

8IGF2
Def

Relative macrocephaly

8DVL3
8CTSK
Def

cathepsin K

8GPC4
#19

Macrocephaly

8TRIP11
Def

Macrocephaly

8RPL5
Def

ribosomal protein L5

8SNX10
Def

Macrocephaly

8D2HGDH
Def

Macrocephaly

8NRAS
Def

Macrocephaly

Possible

604 genes — click to expand
8CTR9
Mod

CTR9 component of Paf1/RNA polymerase II complex

8SHOC2
Def

Relative macrocephaly

8MTM1
Def

Macrocephaly

8EEF2
Mod

eukaryotic translation elongation factor 2

7TCF20
Def

Macrocephaly

7DVL1

Macrocephaly

7MAP2K2
Def

Relative macrocephaly

7POC1A

Macrocephaly

7WDR35
Def

Macrocephaly

7MAPK1

mitogen-activated protein kinase 1

7IDUA
Def

Macrocephaly

7ABCC8
Def

ATP binding cassette subfamily C member 8

7ACVRL1
Def
7AGXT
Def
7B4GALNT1
Def
7CCDC40
Def
7CDK4
Def
7COL6A3
Def
7CYP27B1
Def
7CYP4V2
Def
7DPY19L2
Def
7DRC2
Def
7F11
Def
7GPSM2
Def
7GUSB
Def
7KIF1A
Def
7KIF5A
Def
7KLKB1
Def
7MECOM
Def
7MSRB3
Def
7PLD1
Def
7RDH5
Def
7RPGRIP1
Def
7RSRC1
Def
7RXYLT1
Def
7SCN8A
Def
7SERPINI1
Def
7SLC11A2
Def
7SLC25A4
Def
7SMARCC2
Def
7STAC3
Def
7SUOX
Def
7TBK1
Def
7TERC
Def
7TRAPPC11
Def
7TSFM
Def
7TUBA1A
Def
7SDCCAG8
Def

SHH signaling and ciliogenesis regulator SDCCAG8

7TRIT1
Def

tRNA isopentenyltransferase 1

7B4GALT1
Def

Macrocephaly

7PEX1
Def

Macrocephaly

7PEX6
Def

Macrocephaly

7MT-CYB
Def

mitochondrially encoded cytochrome b

7SHANK3
Def

SH3 and multiple ankyrin repeat domains 3

7AHDC1
Def

Relative macrocephaly

7ASH1L
Def

Macrocephaly

7FOXP1
Def

Macrocephaly

7SON
Def

Macrocephaly

7RAC1
Def

Macrocephaly

6ADK
Def

Macrocephaly

6BOLA2B
6CCDC8
6SLX1A
6SLX1A-SULT1A3
6SULT1A3
6PHF21A
Def

Macrocephaly

6HDAC4
6NRXN3

neurexin 3

6ANKRD17
Def

Macrocephaly

6TMEM216
Def

Macrocephaly

6PAK1
6PPP2CA
Def

Macrocephaly

6DHCR24
Def

Macrocephaly

6RUNX2
6GNB1
Def

Macrocephaly

6CAMTA1
Def

Macrocephaly

6UPF3B
Def

Macrocephaly

6ANO6
Mod
6BLOC1S1
Mod
6CLDN11
Mod
6DDX23
Mod
6EED
Mod
6FAT1
Str
6GFM1
Mod
6LEMD3
6MARS1
Mod
6NCKAP1L
Mod
6NDUFA10
Mod
6PAN2
Mod
6PRIM1
Mod
6RPS26
6STAT6
Str
6PLEC
Def

Macrocephaly

6GNB2
Mod

Macrocephaly

6TNRC6B
Def

Macrocephaly

6ADGRL1
Def

Macrocephaly

6KDM5C
Def

Macrocephaly

6LBR
Mod

Relative macrocephaly

6ZBTB7A

Macrocephaly

6LZTR1
DefSF

Relative macrocephaly

5PIK3R2
Def

Macrocephaly

5TBCK
Def

Macrocephaly

5DLL1
Def

Macrocephaly

5CILK1
Def

Macrocephaly at birth

5CWC27
Def

Macrocephaly

5KDM6B
Def

Relative macrocephaly

5SUFU
Def

Macrocephaly

5RTN4IP1
Def

reticulon 4 interacting protein 1

5TBC1D7

TBC1 domain family member 7

5CCDC186

coiled-coil domain containing 186

5DIPK1A

divergent protein kinase domain 1A

5PLOD1

procollagen-lysine,2-oxoglutarate 5-dioxygenase 1

5MT-ND4
Def

mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 4

5AVIL
Lim
5COX14
Lim
5FMR1
Def

Macrocephaly

5MGCPH

MACROCEPHALY/MEGALENCEPHALY SYNDROME, AUTOSOMAL RECESSIVE; MGCPH

5NFE2
Lim
5PDCD1
Lim
5PDLIM3
Lim
5PDMCS

POLYDACTYLY-MACROCEPHALY SYNDROME; PDMCS

5PRICKLE1
Lim
5PRPH
Lim
5SHMT2
Lim
5TNIK
Lim
5GSK3A

glycogen synthase kinase 3 alpha

5RAB5IF

RAB5 interacting factor

5ZNF526

zinc finger protein 526

5MAX
DefSF

Macrocephaly

5LRP2
No #16

Macrocephaly

5ALG13
Def

Macrocephaly

5CNTNAP2
Def

Macrocephaly

5DST
Def

Macrocephaly

5IFT74
Def

Macrocephaly

5NONO
Def

Macrocephaly

5RIN2
Def

Macrocephaly

5THOC2
Def

Macrocephaly

5RFX7
Def

Macrocephaly

4SPTBN1
Def

Macrocephaly

4CCDC22
Mod

Relative macrocephaly

4IFT81
Mod

Relative macrocephaly

4GRIA3
Def

Macrocephaly

4PCGF2
Def

Macrocephaly

4RNF125

Macrocephaly

4SMPD1
Def

Macrocephaly

4ACKR3
4ACKR5
4ACSL1
4ACTRT3
4ACVR1B
4ADAMTS20
4ADCY6
4ADCY6-DT
4AGAP1
4AGAP2
4AMHR2
4AMIGO2
4ANKMY1
4ANKRD33
4ANKRD37
4ANKRD52
4ANO7
4ANP32D
4AQP12A
4AQP12B
4AQP2
4AQP5
4AQP6
4ARF3
4ARHGAP9
4ARHGEF25
4ARL14
4ASB1
4ASB18
4ASB8
4ASIC1
4ATF1
4ATF7
4ATF7-NPFF
4ATG101
4ATG4B
4ATP23
4ATP5F1B
4ATP5MC2
4AVPR1A
Dis
4B3GALNT1
4BAZ2A
4BCDIN3D
4BIN2
4BLOC1S1-RDH5
4BOLA2
4BOLA2-SMG1P6
4C12ORF54
4C12ORF56
4C1QL4
4C3ORF80
4CACNB3
4CALCOCO1
4CAPN10
4CAPN10-DT
4CASP3
4CBX5
4CCDC110
4CCDC184
4CCNT1
4CD63
4CDK2
4CDKN2AIP
4CELA1
4CENPU
4CERS5
4CFAP96
4CFAP97
4CISTR
4CLDN22
4CLDN24
4CNPY2
4COPS8
4COPS8-DT
4COPS9
4COPZ1
4COQ10A
4COXFA4L2
4CROCC2
4CSRNP2
4CTDSP2
4DAZAP2
4DBX2
4DCTN2
4DDIT3
4DIP2B
4DNAJC14
4DNAJC22
4DRC11
4DTX3
4DTYMK
4DUSP28
4EEF1AKMT3
4EIF4B
4EIF5A2
4ENDOU
4ENPP6
4ERBB3
4ESPL1
4ESPNL
4ESYT1
4FAIM2
4FAM149A
4FAM186A
4FAM186B
4FAM240C
4FAM242C
4FARP2
4FBXO36
4FIGNL2
4FIGNL2-DT
4FKBP11
4FLJ38576
4FMNL3
4FRA12A
4FRG1
4FRG1-DT
4FRG2
4FSD1L
4GAL3ST2
4GALNT6
4GBX2
4GDF11
4GIHCG
4GLI1
4GLS2
4GOLIM4
4GPC1
4GPD1
4GPR160
4GPR35
4GPR84
4GTSF1
4GXYLT1
4H1-7
4HDAC7
4HDLBP
4HES6
4HIGD1C
4HNRNPA1
4HOTAIR
4HOXC10
4HOXC11
4HOXC12
4HOXC13
4HOXC4
4HOXC5
4HOXC6
4HOXC8
4HOXC9
4HSD17B6
4IFT54
4IGFBP6
4IKZF4
4IL12A
4IL23A
4ILKAP
4ING2
4ING2-DT
4ING5
4INHBC
4INHBE
4IQCJ-SCHIP1
4IRAK4
4IRF2
4IRF2-DT
4ITGA5
4ITGA7
4ITGB7
4KANSL2
4KCNH3
4KICS2
4KLHL30
4KPNA4
4KRT1
4KRT18
4KRT2
4KRT3
4KRT4
4KRT5
4KRT6A
4KRT6B
4KRT6C
4KRT7
4KRT71
4KRT72
4KRT73
4KRT74
4KRT75
4KRT76
4KRT77
4KRT78
4KRT79
4KRT8
4KRT80
4KRT81
4KRT82
4KRT83
4KRT84
4KRT85
4KRT86
4LACRT
4LALBA
4LARP4
4LETMD1
4LIMA1
4LMBR1L
4LRIG3
4LRIG3-DT
4LRP1
4LRP2BP
4LRRC31
4LRRC34
4LRRFIP1
4LRRIQ4
4MAB21L4
4MAP3K12
4MARCHF9
4MBD6
4MCRS1
4METTL1
4MFSD1
4MIRLET7I
4MIRLET7IHG
4MLDHR
4MLF1
4MLF1-DT
4MMP19
4MON2
4MTERF4
4MTNR1A
4MUCL1
4MYG1
4MYL6
4MYL6B
4MYO1A
Ref
4NAB2
4NABP2
4NCKAP5L
4NELL2
4NEMP1
4NEU4
4NEUROD4
4NMD3
4NPIPB12
4NPIPB13
4NR4A1
4NR4A1AS
4NXPH4
4OR10A7
4OR10AD1
4OR10P1
4OR2AP1
4OR5BS1
4OR6B2
4OR6B3
4OR6C1
4OR6C2
4OR6C3
4OR6C4
4OR6C6
4OR6C65
4OR6C68
4OR6C70
4OR6C74
4OR6C75
4OR6C76
4OR8S1
4OR9K2
4ORI6
4ORMDL2
4OS9
4OTOL1
4PA2G4
4PCBP2
4PCBP2-OT1
4PCED1B
4PDCD10
4PDE1B
4PDZRN4
4PER2
4PFDN5
4PHC3
4PIP4K2C
4PLAG1
4POU6F1
4PPHLN1
4PPM1H
4PPM1L
4PPM1L-DT
4PPP1R1A
4PPP1R7
4PRIMPOL
4PRKAG1
4PRKCI
4PRPF40B
4PRR13
4PRR21
4PTGES3
4PUS7L
4PYM1
4R3HDM2
4R3HDM2-DT
4RAB17
4RAB17-DT
4RAB5B
4RACGAP1
4RAMP1
4RAPGEF3
4RARRES1
4RASSF3
4RBM44
4RBMS2
4RDH16
4RHEBL1
4RND1
4RNF41
4RNPEPL1
4RPAP3
4RPAP3-DT
4RPL22L1
4RPL41
4RTP5
4RWDD4
4SAMD7
4SARNP
4SCAF11
4SCARNA7
4SCAT2
4SCHIP1
4SDR9C7
4SEC62
4SENP1
4SEPTIN2
4SERPINI2
4SLC16A7
4SLC2A2
4SLC38A1
4SLC38A2
4SLC38A4
4SLC39A5
4SLC48A1
4SLC4A4
4SLC4A8
4SLC61A1
4SLC7A14
Dis
4SLITRK3
4SLX1B
4SLX1B-SULT1A4
4SMAGP
4SMARCD1
4SMC4
4SMIM41
4SMUG1
4SNED1
4SNORA105C
4SNORA2A
4SNORA2B
4SNORA2C
4SNX25
4SOAT2
4SORBS2
4SP1
4SP7
4SPATS2
4SPMIP11
4SPRYD3
4SPRYD4
4SPTSSB
4SRGAP1
4STAT2
4STK25
4STOX2
4SULT1A4
4SUPT16H
4TAC3
4TAFA2
4TAMALIN
4TANAR
4TARBP2
4TBC1D30
4TENM3
4TESPA1
4TFCP2
4THAP4
4TIMELESS
4TLR3
4TMBIM6
4TMDD1
4TMEM106C
4TMEM117
4TMPRSS12
4TMT1A
4TMT1B
4TNS2
4TRIM59
4TRIM59-IFT80
4TRIML1
4TRIML2
4TROAP
4TRS-CGA4-1
4TRV-AAC1-1
4TSPAN31
4TUBA1B
4TUBA1C
4TWF1
4TWIST2
4UBE2F
4UBE2F-SCLY
4UC.134
4UFSP2
4UICLM
4USP15
4WDR49
4WIF1
4WNT1
4WNT10B
4WWC2
4YAF2
4ZBTB39
4ZC3H10
4ZCRB1
4ZFP42
4ZNF385A
4ZNF641
4ZNF740
4BICD2

BICD cargo adaptor 2

4GALNT8

polypeptide N-acetylgalactosaminyltransferase 8

4KCNA6

potassium voltage-gated channel subfamily A member 6

4GNE
Def

Macrocephaly

4POR
Def

Macrocephaly

4B3GLCT
Def

Macrocephaly

4CAMK2A
Def

Macrocephaly

4NDUFAF3
Def

Macrocephaly

4APC2
Str

Macrocephaly

4KCNH1
Def

Macrocephaly

4KMT5B
Def

Macrocephaly

4ZSWIM6
Def

Macrocephaly

3ROR2

Macrocephaly

3HECTD4

Macrocephaly

3CSGALNACT1
Mod

Macrocephaly

3PDGFRB

Macrocephaly

3B4GALT7
Def

Macrocephaly

3CRPPA
Def

Macrocephaly

3DAG1
Def

Macrocephaly

3DOCK6
Def

Macrocephaly

3DYNC2I1
Def

Macrocephaly

3ETFA
Def

Macrocephaly

3ETFDH
Def

Macrocephaly

3HUWE1
Def

Macrocephaly

3KCNJ1
Def

Macrocephaly

3LRP4
Def

Macrocephaly

3MAN2B1
Def

Macrocephaly

3MOCS2
Def

Macrocephaly

3MSX2
Def

Macrocephaly

3MYMK
Def

Macrocephaly

3NDUFS4
Def

Progressive macrocephaly

3PIGA
Def

Macrocephaly

3SMO
Def

Macrocephaly

Related phenotype searches

Intellectual disabilityGlobal developmental delaySpeech/language delayNeurodegenerationDevelopmental regressionSeizuresEpileptic encephalopathyStatus epilepticus

Data aggregated from HPO/Monarch, ClinVar, OMIM (phenotypes + clinical synopsis), Open Targets, PanelApp, Phen2Gene, and Gene2Phenotype. Click a gene to view full details.