Genes associated with “macrocephaly”

Diagnostic yield calculator →
323 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

17 genes
1
NF1 →

neurofibromin 1

38
score
ClinGen: DefinitiveGTR ↑

Macrocephaly

Frequency
38%
n=128
P/LP Variants
10
OT Score
0.27
2
PTEN →

phosphatase and tensin homolog

38
score
ClinGen: DefinitiveACMG SFP2G #2GTR ↑

Postnatal macrocephaly

Frequency
100%
n=3
P/LP Variants
33
OT Score
0.56
3
35
score
ClinGen: DefinitiveGTR ↑

Macrocephaly

Frequency
88%
n=131
P/LP Variants
5
OT Score
-
4
CHD3 →

chromodomain helicase DNA binding protein 3

33
score
ClinGen: DefinitiveGTR ↑

Macrocephaly

Frequency
61%
n=31
P/LP Variants
5
OT Score
0.37
5
GLI3 →

GLI family zinc finger 3

32
score
ClinGen: DefinitiveP2G #3GTR ↑

Macrocephaly

Frequency
0%
n=10
P/LP Variants
12
OT Score
0.12
6
PTCH1 →

patched 1

31
score
ClinGen: DefinitiveP2G #9GTR ↑

Macrocephaly

Frequency
-
P/LP Variants
112
OT Score
0.33
7
MTOR →

mechanistic target of rapamycin kinase

31
score
ClinGen: DefinitiveGTR ↑

Macrocephaly

Frequency
100%
n=4
P/LP Variants
3
OT Score
0.29
8
CHD8 →

chromodomain helicase DNA binding protein 8

29
score
ClinGen: DefinitiveGTR ↑
Frequency
-
P/LP Variants
10
OT Score
0.41
9
27
score
ClinGen: DefinitiveP2G #29GTR ↑

Relative macrocephaly

Frequency
78%
n=9
P/LP Variants
3
OT Score
-
27NFIX
Def

Macrocephaly

27BRWD3
Def

Macrocephaly

25FGFR3
Def#1

Macrocephaly

25NFIA
Def

Macrocephaly

23ASPA
Def#12

Macrocephaly

22DICER1
Def

Macrocephaly

21GUSB
Def

Macrocephaly

20EZH2
Def#5

Consider

97 genes
20NFIB
Def

nuclear factor I B

20TCIRG1
Def

Macrocephaly

20INPPL1
Def

Relative macrocephaly

19NSD1
Def#7

Macrocephaly

19KPTN
Def

Macrocephaly

19SPRED1
Def
18ZBTB20
Def

Macrocephaly

18MLC1
Def

modulator of VRAC current 1

17ZBTB7A

Macrocephaly

16PIK3CA
Ref#13

Progressive macrocephaly

14KIF7
#4
14KMT2E
Def

Macrocephaly

13GPC4
#19

Macrocephaly

13ERF
Def

Macrocephaly

13HSD17B4
Def

Macrocephaly

13AGA
Def
13COMMAD

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

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

13SUFU
Def
13TET3
Def
13TRIO
Def
13TRIP12
Def
13DNMT3A
Def

Macrocephaly

12DVL1

Macrocephaly

12FOXP1
Def

Macrocephaly

12FBN1
DefSF

Macrocephaly

11DVL3

Macrocephaly

11CHD4
Def

Macrocephaly

11AMER1
Def
11CORO1A
Def
11OBSL1

Relative macrocephaly

11PRRT2
Def
11PTCH2
Lim
11CACNA1E
Def

Macrocephaly

11SHANK3
Def

Macrocephaly

11KRAS
Def#6

Macrocephaly

11WNT5A
Mod
10BRAF
Def

Macrocephaly

10MAPK3
10STXBP1
Def

syntaxin binding protein 1

10RPS6KA3
Def

ribosomal protein S6 kinase A3

10SATB2
Def

SATB homeobox 2

10SPATA22
10OFD1
Def

Macrocephaly

10TBC1D7

Macrocephaly

10SOS1
Def

Macrocephaly

10AKT3
Def

AKT serine/threonine kinase 3

9FAM111A
Def
9ARSB
Def

Macrocephaly

9WDFY3
Def

WD repeat and FYVE domain containing 3

9ARID1B
Def
9CDKL5
Def
9KANSL1
Def
9MEF2C
Def
9TBL1XR1
Def
9ZMYND11
Def
9FAM177A1

Macrocephaly

9ACAN
Def

Relative macrocephaly

9PPP1CB
Def

Macrocephaly

8IGF2
Def

Relative macrocephaly

8CTSK
Def

cathepsin K

8EXT2
Def

Macrocephaly

8RAB39B
Def

Macrocephaly

8HEPACAM
Def

Macrocephaly

8TAOK1
Def

Macrocephaly

8ITCH
Def

Relative macrocephaly

8ABCC9
Def

ATP binding cassette subfamily C member 9

8RPL5
Def

ribosomal protein L5

8ALDOA
8ASPHD1
8C16ORF54
8CDIPT
8CDIPTOSP
8DOC2A
8FIMP1
8GDPD3
8HIRIP3
8INO80E
8KCTD13
8KCTD13-DT
8KIF22
8MVP-DT
8PAGR1
8PPP4C
8SEZ6L2
8TAOK2
8TBX6
8TLCD3B
8TMEM219
8YPEL3
8YPEL3-DT
8ZG16

Possible

169 genes — click to expand
8CTR9
Mod

CTR9 component of Paf1/RNA polymerase II complex

8AHDC1
Def

Macrocephaly

8SHOC2
Def

Relative macrocephaly

7MITF
Def

Macrocephaly

7OPHN1
Def

Macrocephaly

7MAPK1

mitogen-activated protein kinase 1

7ABCC8
Def

ATP binding cassette subfamily C member 8

7CCDC40
Def
7CYP4V2
Def
7F11
Def
7HMGA2
Def
7KLKB1
Def
7PHOX2B
Def
7SLC25A4
Def
7TCF7L2
Def
7TRAPPC11
Def
7TRIT1
Def

tRNA isopentenyltransferase 1

7B4GALT1
Def

Macrocephaly

7PEX1
Def

Macrocephaly

7MT-CYB
Def

mitochondrially encoded cytochrome b

7PLCB4
Def

Macrocephaly

7DEPDC5
Def

Macrocephaly

7AKT1
Lim#8

Macrocephaly

7INPP5E
Def

Macrocephaly

7KDM6B
Def

Macrocephaly

7ASH1L
Def

Macrocephaly

7SON
Def

Macrocephaly

7RAC1
Def

Macrocephaly

6BOLA2B
6CCDC8
6ODC1
6SLX1A
6SLX1A-SULT1A3
6SULT1A3
6PHF21A
Def

Macrocephaly

6NRXN3

neurexin 3

6ANKRD17
Def

Macrocephaly

6GNB1
Def

Macrocephaly

6FAT1
Str
6EML1
Def

Macrocephaly

6ADGRL1
Def

Macrocephaly

6MECP2
Def

Macrocephaly

6EEF2

eukaryotic translation elongation factor 2

6LBR
Mod

Macrocephaly

5PIK3R2
Def

Macrocephaly

5TBCK
Def

Macrocephaly

5DLL1
Def

Macrocephaly

5CDH2
Def

Macrocephaly

5PLG
Def

Macrocephaly

5EIF2B1
Def

Macrocephaly

5RTN4IP1
Def

reticulon 4 interacting protein 1

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

5COL2A1
Def

Macrocephaly

5CUL4B
Def

Relative macrocephaly

5MGCPH

MACROCEPHALY/MEGALENCEPHALY SYNDROME, AUTOSOMAL RECESSIVE; MGCPH

5PDLIM3
Lim
5SETD2
Def

Postnatal macrocephaly

5SYN1
Def

Macrocephaly

5GSK3A

glycogen synthase kinase 3 alpha

5RAB5IF

RAB5 interacting factor

5ZNF526

zinc finger protein 526

5LAMA5
Def

Relative macrocephaly

5NONO
Def

Relative macrocephaly

5TMCO1

Macrocephaly

5GAN
Def

Macrocephaly

5GNS
Def

Macrocephaly

5HECW2
Def

Macrocephaly

5RIN2
Def

Macrocephaly

5THOC2
Def

Macrocephaly

5RFX7
Def

Macrocephaly

4SPTBN1
Def

Macrocephaly

4CCDC22
Mod

Relative macrocephaly

4MAB21L2
Def

Macrocephaly

4TRAF7
Def

Macrocephaly

4GNAI3
Mod

Macrocephaly

4CEP120
Def

Relative macrocephaly

4GRIA3
Def

Macrocephaly

4NDUFV1
Def

Macrocephaly

4PCGF2
Def

Macrocephaly

4ROBO3
Def

Macrocephaly

4RERE
Def

Macrocephaly

4SMPD1
Def

Macrocephaly

4ACSL1
4ANKRD37
4BOLA2
4BOLA2-SMG1P6
4CASP3
4CCDC110
4CDKN1C
Str

Macrocephaly

4CDKN2AIP
4CENPU
4CFAP96
4CFAP97
4CLDN22
4CLDN24
4CRHR1
4CUL7
4ENPP6
4FAM149A
4FLJ38576
4FRG1
4FRG1-DT
4FRG2
4HERC1
4ING2
4ING2-DT
4IRF2
4IRF2-DT
4LRP2BP
4MAPT-IT1
4MTNR1A
4NPIPB12
4NPIPB13
4POC1A
4PRIMPOL
4RWDD4
4SLX1B
4SLX1B-SULT1A4
4SNX25
4SORBS2
4SPPL2C
4STOX2
4SULT1A4
4TENM3
4TLR3
4TRIML1
4TRIML2
4UFSP2
4WWC2
4ZFP42
4BICD2

BICD cargo adaptor 2

4GALNT8

polypeptide N-acetylgalactosaminyltransferase 8

4KCNA6

potassium voltage-gated channel subfamily A member 6

4JARID2
Def

Macrocephaly

4KDM1A
Def

Macrocephaly

4B3GLCT
Def

Macrocephaly

4SUZ12

Macrocephaly

4CAMK2A
Def

Macrocephaly

4NDUFAF3
Def

Macrocephaly

4UBE2A
Def

Macrocephaly

4USP9X
Def

Relative macrocephaly

4APC2
Str

Macrocephaly

4MRAS
Mod

Relative macrocephaly

4KMT5B
Def

Macrocephaly

4KCNC2
Def

Macrocephaly

4MSX2
Def

Macrocephaly

4GAD1
Def

Macrocephaly

3POLE
DefSF

Relative macrocephaly

3IFT43
Mod

Macrocephaly

3SEC24D

Macrocephaly

3BBS1
Def

Macrocephaly

3BLTP1
Def

Macrocephaly

3CRPPA
Def

Macrocephaly

3D2HGDH
Def

Macrocephaly

3DOCK6
Def

Macrocephaly

3ETFA
Def

Macrocephaly

3ETFB
Def

Macrocephaly

3HUWE1
Def

Macrocephaly

3LRP4
Def

Macrocephaly

3MAN2B1
Def

Macrocephaly

3MOCS1
Def

Macrocephaly

3NDUFS4
Def

Progressive macrocephaly

3PIGN
Def

Macrocephaly

3SEC23B
Def

Macrocephaly

3SLC25A1
Def

Macrocephaly

3TMEM94
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.