Genes associated with “microcephaly”

377 genes foundHPO: MicrocephalyOpen Targets: microcephaly1 PanelApp panel
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

57 genes
1
KIF11 →

kinesin family member 11

56
score
ClinGen: DefinitivePanel: Green ↑GTR ↑
Frequency
-
P/LP Variants
5
OT Score
0.82
2
CEP152 →

centrosomal protein 152

51
score
ClinGen: DefinitivePanel: Green ↑P2G #30GTR ↑
Frequency
-
P/LP Variants
52
OT Score
0.79
3
MCPH1 →

microcephalin 1

47
score
ClinGen: DefinitivePanel: Green ↑GTR ↑
Frequency
-
P/LP Variants
5
OT Score
0.81
4
ASPM →

assembly factor for spindle microtubules

47
score
ClinGen: DefinitivePanel: Green ↑GTR ↑
Frequency
-
P/LP Variants
7
OT Score
0.79
5
WDR62 →

WD repeat domain 62

45
score
ClinGen: DefinitivePanel: Green ↑GTR ↑
Frequency
-
P/LP Variants
3
OT Score
0.82
6
CDK5RAP2 →

CDK5 regulatory subunit associated protein 2

45
score
ClinGen: DefinitivePanel: Green ↑GTR ↑

Primary microcephaly

Frequency
100%
n=2
P/LP Variants
1
OT Score
0.81
7
NDE1 →

nudE neurodevelopment protein 1

44
score
ClinGen: DefinitivePanel: Green ↑GTR ↑
Frequency
-
P/LP Variants
54
OT Score
0.81
8
TUBGCP6 →

tubulin gamma complex component 6

42
score
ClinGen: DefinitivePanel: Green ↑GTR ↑

Microcephaly

Frequency
-
P/LP Variants
1
OT Score
0.80
9
SLC25A19 →

solute carrier family 25 member 19

42
score
ClinGen: LimitedPanel: Green ↑GTR ↑

Primary microcephaly

Frequency
100%
n=11
P/LP Variants
18
OT Score
0.79
41STIL
DefP:G

STIL centriolar assembly protein

38PNKP
DefP:G

polynucleotide kinase 3'-phosphatase

37PCNT
DefP:G

Microcephaly

37NBN
DefP:G#3

Microcephaly

34LMNB1
DefP:G

lamin B1

34DYRK1A
DefP:G

Primary microcephaly

32KNL1
P:G

kinetochore scaffold 1

32KIF14
P:G

Microcephaly

32LMNB2
P:G

lamin B2

32MFSD2A
P:G

Microcephaly

30RNU4ATAC
DefP:G

Microcephaly

30DHCR7
DefP:G#5
30TRIO
DefP:G

Microcephaly

30MECP2
DefP:G

Progressive microcephaly

29ZNF335
P:G

zinc finger protein 335

29TUBGCP4
P:G

tubulin gamma complex component 4

28NIPBL
DefP:G
27SMC1A
DefP:G#17

Microcephaly

26BRIP1
DefP:G
26HDAC8
DefP:G#15
26PQBP1
DefP:G
26FANCC
DefP:G
26CEP135
P:G

Primary microcephaly

25FANCG
DefP:G
25FANCA
DefP:G
25RTTN
DefP:G

rotatin

25ASNS
Def
24RBBP8
P:G#12

RB binding protein 8, endonuclease

24FANCI
DefP:G
24SMC3
DefP:G
23FOXG1
DefP:G
23RAD21
DefP:G
23NCAPD2
P:G

non-SMC condensin I complex subunit D2

23ANKLE2
P:G

ankyrin repeat and LEM domain containing 2

23ZEB2
DefP:G
22TSEN54
P:G

Progressive microcephaly

22ERCC4
DefP:G
22BUB1
LimP:G

BUB1 mitotic checkpoint serine/threonine kinase

21NCAPD3
P:G

non-SMC condensin II complex subunit D3

21SLX4
DefP:G
21CASK
DefP:G
21UBE3A
DefP:A
20VPS13B
Def#8

vacuolar protein sorting 13 homolog B

20EFTUD2
DefP:G
20POGZ
DefP:G
20ERCC6
DefP:G#20

Microcephaly

20ARCN1
P:A
20VARS1
Def

Consider

90 genes
20BUB1B
DefP:G

Microcephaly

20PAH
Def
20RAD51C
DefP:A
19EP300
Def#18

Microcephaly

19FANCM
DefP:R
19BPTF
DefP:G

bromodomain PHD finger transcription factor

18DIAPH1
DefP:G
18FANCL
DefP:G
18AKT3
DefP:A
18BRCA2
DefSFP:G

Microcephaly

18ARID1B
Def#1

Microcephaly

18TTI1
P:G

Microcephaly

17CDK6
P:R

cyclin dependent kinase 6

17RAD50
RefP:G
17FANCF
DefP:G

Microcephaly

16MORC2
DefP:G

MORC family CW-type zinc finger 2

16SASS6
P:G

SAS-6 centriolar assembly protein

16SMARCA5
ModP:G

SNF2 related chromatin remodeling ATPase 5

16ARID1A
Def#9

Microcephaly

16CSNK2A1
DefP:G

Microcephaly

16KCNT1
Def

Microcephaly

15WDR11
P:G

WD repeat domain 11

15PDHA1
DefP:G

Microcephaly

15ARF3
P:G

ARF GTPase 3

15ESCO2
Def#14

Microcephaly

15TRMT10A
P:G
15CTCF
DefP:G
15GRIN2B
Def
15SLC9A6
DefP:G
15ASXL1
Def
15PLK4
P:G

polo like kinase 4

14NSD1
Def
14PHC1
P:R

polyhomeotic homolog 1

14POC1A
P:G

Microcephaly

14COPB2
P:R

Microcephaly

14MED17
P:A
14ERCC5
DefP:A

Microcephaly

14PPFIBP1
P:G

PPFIB scaffold protein 1

14VRK1
P:G

Microcephaly

14BLM
DefP:G

Microcephaly

14TNPO2
P:G

transportin 2

14NUP37

nucleoporin 37

13DONSON
P:G

Microcephaly

13AP4M1
DefP:A
13BRD4
DefP:A
13TP53
DefSF

Microcephaly

13EPG5
Def
13MCLMR

MICROCEPHALY WITH OR WITHOUT CHORIORETINOPATHY, LYMPHEDEMA, OR IMPAIRED INTELLECTUAL DEVELOPMENT; MCLMR

13MICPCH

INTELLECTUAL DEVELOPMENTAL DISORDER WITH MICROCEPHALY AND PONTINE AND CEREBELLAR HYPOPLASIA; MICPCH

13MMACHC
Def
13MTHFR
Def
13MTRR
Def
13PHGDH
Def
13ZIC2

Microcephaly

12WDFY3
DefP:R

Microcephaly

12CENPF
P:G
12NARS1
Mod
12MMADHC
Def
12MCM7
P:A

minichromosome maintenance complex component 7

12PPP2R1A
Def
11RARS2
Def

Microcephaly

11DYNC1H1
Def
11NSD2
DefP:G

Microcephaly

11WDR4
P:G

Microcephaly

10NCAPH
P:R

non-SMC condensin I complex subunit H

10SLC16A2
Def

Microcephaly

10RAB3GAP2
Def

Microcephaly

10SIN3A
Def

Microcephaly

10AOPEP
10CZ1P-ASNS
10PUS7
P:G
10SLF2
P:G
10SMC5
P:G
10TMEM167A
P:G
10TAF2

Microcephaly

9AFG2A
Def
9SCN3A
Def
9SMARCA2
Def
9CHD7
Def
9DDX41
Def
9DPM1
DefP:G

Secondary microcephaly

9NHS
Def
9KAT6A
Def

Microcephaly

9TERT
Def

Microcephaly

8GTF3C3
P:G

Microcephaly

8CLASP1

cytoplasmic linker associated protein 1

8POLE
DefSF

Microcephaly

8PEX7
Def

Microcephaly

8SNHG14
8XPA
Def

Microcephaly

Possible

183 genes — click to expand
8COG3
LimP:A

Microcephaly

8TRAPPC14

trafficking protein particle complex subunit 14

8EMG1
Str

Microcephaly

8TBCD
Def

Secondary microcephaly

7PTPMT1
P:A

Microcephaly

7EXOC7
ModP:A

Microcephaly

7PSMC1

Microcephaly

7AFG3L2
Def
7B4GALT7
Def
7F12
Def
7FAM111A
Def
7GABRB3
Def
7GTPBP2
Def
7LMBRD1
Def
7MAGEL2
Def
7MSH6
DefSF
7OCA2
Def
7PAK3
Def
7SLC34A1
Def
7SMAD6
Def
7XPC
Def
7ASXL3
Def

Microcephaly

7CARS1

Microcephaly

7PLP1
Def

Microcephaly

7THOC2
Def

Microcephaly

7DDX3X
Def

Microcephaly

6ATP1A3
Def

Microcephaly

6LINS1
Def

Microcephaly

6POMT2
Def

Microcephaly

6TM2D3
P:A

Microcephaly

6TUBB2B
Def

Microcephaly

6ZNF276
6ALG9
Def

Microcephaly

6FAT1
Str
6HYLS1
Mod
6SYNGAP1
Def

Microcephaly

6SPTAN1
Def

Microcephaly

6ADAT3
Mod

Microcephaly

6CENPE
LimP:R

Primary microcephaly

6CTSD
Def

Microcephaly

6HNRNPR
Def

Secondary microcephaly

6MICOS13
Def

Secondary microcephaly

5EEF1A2
Def

Microcephaly

5GMPPB
Def

Microcephaly

5STT3A
Def

Microcephaly

5RPS19
Def

Microcephaly

5BCAS3

Microcephaly

5MAPK1

Microcephaly

5WWOX
Def

Secondary microcephaly

5CDK16
Lim
5FGFR1
Def

Microcephaly

5KMT2C
Def

Microcephaly

5MCPHA

MICROCEPHALY, AMISH TYPE; MCPHA

5MEIS2
Def

Microcephaly

5NEDMISBA

NEURODEVELOPMENTAL DISORDER WITH PROGRESSIVE MICROCEPHALY, SPASTICITY, AND BRAIN IMAGING ABNORMALITIES; NEDMISBA

5ROBO1
Lim
5SEPSECS

Progressive microcephaly

5XRCC2
Lim
5ZC4H2
Def

Microcephaly

5FAR1
Mod

Microcephaly

5KCNK3
Def

Microcephaly

5SPTBN1
Def

Microcephaly

5GABRA2

Microcephaly

5KIF1A
Def

Microcephaly

5GORAB
Def

Microcephaly

5ALG13
Def

Microcephaly

5COG4
Def

Microcephaly

5LGI1
Def

Primary microcephaly

5SLC30A9
Def

Microcephaly

5TRIM8
Def

Microcephaly

5CLPP
Def

Microcephaly

4MPV17
Def

Microcephaly

4GRIA2
Def

Progressive microcephaly

4FKRP
Def

Microcephaly

4NDUFS4
Def

Microcephaly

4SPR
Def

Microcephaly

4BRF1

Microcephaly

4ARL10
4ATP10A
4ATP10A-DT
4CDHR2
4CDK19
4CTBP1
4CYFIP1
4DBN1
4DENND5A
4DOK3
4EIF4E1B
4FAF2
4FAM153A
4FAM153B
4FAM193B
4FARSB
4FBXO11
4FGFR4
4GABRA5
4GABRG3
4GOLGA6L1
4GOLGA6L2
4GOLGA6L26
4GOLGA8S
4GPRIN1
4GRK6
4HERC2
4HIGD2A
4HK3
4KATNB1
4KIAA1191
4LMAN2
4MKRN3
4MXD3
4NIPA1
4NIPA2
4NOP16
4NPAP1
4PDLIM7
4PFN3
4PLEKHG2
4PRELID1
4PRR7
4PUS3
4PWAR1
4PWAR4
4PWAR5
4PWAR6
4PWARSN
4PWRN1
4PWRN2
4PWRN3
4PWRN4
4PYCR2
4RAB24
4RABGAP1
4REPS2
4RGS14
4RNF44
4SIMC1
4SMPD4
4SNRPN
4SNURF
4TMED9
4TRE-TTC2-2
4TSPAN17
4TUBGCP5
4UIMC1
4UNC5A
4YWHAE
4ZNF346
4NDUFS1
Def

Microcephaly

4PIGO
Def

Microcephaly

4ALG2
Str

Microcephaly

4PLPBP

Secondary microcephaly

4CACNA1G
Def

Microcephaly

4KLHL20
Mod

Microcephaly

4HIVEP2

Secondary microcephaly

4ACSL4
Def

Microcephaly

4PRORP
Def

Secondary microcephaly

4NDUFA11
Lim

Secondary microcephaly

3JARID2
Def

Microcephaly

3PIDD1
Def

Microcephaly

3DRG1

Microcephaly

3GOT2

Progressive microcephaly

3HMGCL
Def

Microcephaly

3DDX59

Microcephaly

3BRAT1
Def

Progressive microcephaly

3CPT2
Def

Microcephaly

3ELOVL4
Def

Microcephaly

3GBA1
Def

Microcephaly

3LRP5
Def

Microcephaly

3MASP1
Def

Microcephaly

3MBD5
Def

Microcephaly

3MOCS1
Def

Microcephaly

3POMGNT1
Def

Microcephaly

3PPT1
Def

Progressive microcephaly

3PRKDC
Def

Microcephaly

3PSAT1
Def

Secondary microcephaly

3RNASEH2A
Def

Progressive microcephaly

3SERAC1
Def

Microcephaly

3SET
Def

Microcephaly

3ST3GAL5
Def

Microcephaly

3TREX1
Def

Progressive microcephaly

3VARS2
Def

Microcephaly

3VPS33B
Def

Microcephaly

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.