Genes associated with “microcephaly”

Diagnostic yield calculator →
438 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

56 genes
1
KIF11 →

kinesin family member 11

56
score
ClinGen: DefinitivePanel: Green ↑GTR ↑
Frequency
-
P/LP Variants
10
OT Score
0.82
2
MCPH1 →

microcephalin 1

53
score
ClinGen: DefinitivePanel: Green ↑GTR ↑

MICROCEPHALY 1, PRIMARY, AUTOSOMAL RECESSIVE; MCPH1

Frequency
-
P/LP Variants
6
OT Score
0.81
3
LMNB1 →

lamin B1

52
score
ClinGen: DefinitivePanel: Green ↑GTR ↑

Microcephaly

Frequency
100%
n=13
P/LP Variants
14
OT Score
0.74
4
WDR62 →

WD repeat domain 62

47
score
ClinGen: DefinitivePanel: Green ↑GTR ↑
Frequency
-
P/LP Variants
7
OT Score
0.81
5
ASPM →

assembly factor for spindle microtubules

47
score
ClinGen: DefinitivePanel: Green ↑GTR ↑
Frequency
-
P/LP Variants
8
OT Score
0.79
6
STIL →

STIL centriolar assembly protein

47
score
ClinGen: DefinitivePanel: Green ↑GTR ↑
Frequency
-
P/LP Variants
30
OT Score
0.79
7
CDK5RAP2 →

CDK5 regulatory subunit associated protein 2

46
score
ClinGen: DefinitivePanel: Green ↑GTR ↑
Frequency
-
P/LP Variants
4
OT Score
0.80
8
CEP152 →

centrosomal protein 152

45
score
ClinGen: DefinitivePanel: Green ↑P2G #30GTR ↑
Frequency
-
P/LP Variants
1
OT Score
0.80
9
TUBGCP6 →

tubulin gamma complex component 6

41
score
ClinGen: DefinitivePanel: Green ↑GTR ↑
Frequency
-
P/LP Variants
1
OT Score
0.79
38PCNT
DefP:G

pericentrin

38NDE1
DefP:G

nudE neurodevelopment protein 1

38PNKP
DefP:G

polynucleotide kinase 3'-phosphatase

37DYRK1A
DefP:G

Primary microcephaly

36BUB1
LimP:G

Primary microcephaly

35SLC25A19
LimP:G

solute carrier family 25 member 19

34RTTN
DefP:G

Microcephaly

34KIF14
P:G

Microcephaly

33RNU4ATAC
DefP:G

Microcephaly

31PLK4
P:G

Microcephaly

31NBN
DefP:G#3
30DHCR7
DefP:G#5
30CASK
DefP:G

Microcephaly

30MECP2
DefP:G

Progressive microcephaly

29TUBGCP4
P:G

tubulin gamma complex component 4

29ZNF335
P:G

zinc finger protein 335

28FOXG1
DefP:G
28NIPBL
DefP:G
27SMC3
DefP:G

Primary microcephaly

26FANCA
DefP:G

Microcephaly

26ZEB2
DefP:G
26HDAC8
DefP:G#15
26FANCC
DefP:G
25FANCG
DefP:G
25ASNS
Def
25CEP135
P:G

centrosomal protein 135

25NCAPD2
P:G

non-SMC condensin I complex subunit D2

25SMC1A
DefP:G#17

Microcephaly

24RBBP8
P:G#12

RB binding protein 8, endonuclease

24NCAPD3
P:G

non-SMC condensin II complex subunit D3

23QARS1
Def

Progressive microcephaly

23RAD21
DefP:G
23ARFGEF2
Def

Microcephaly

23UBE3A
DefP:A
23ANKLE2
P:G

ankyrin repeat and LEM domain containing 2

23KAT6B
Def#7

Microcephaly

22SLC1A4
DefP:G

Microcephaly

22FANCI
DefP:G
21PPFIBP1
P:G

PPFIB scaffold protein 1

21SLX4
DefP:G
21CTCF
DefP:G
21EFTUD2
DefP:G
21POGZ
DefP:G
21PAH
Def

Microcephaly

21VPS13B
Def#8

vacuolar protein sorting 13 homolog B

20CTNNB1
DefP:G
20ARCN1
P:A

Consider

110 genes
20ASXL1
Def
20FANCD2
DefP:G
20BUB1B
DefP:G

Microcephaly

20TTI1
P:G

Microcephaly

20RAD51C
DefP:A
19EP300
Def#18

Microcephaly

19SLC9A6
DefP:G
19TRIO
DefP:G
19ERCC8
DefP:G

Microcephaly

19BPTF
DefP:G

bromodomain PHD finger transcription factor

19DIAPH1
DefP:G

Microcephaly

18AKT3
DefP:A
18PHC1
P:R

Microcephaly

18ASXL3
Def

Microcephaly

17CDK6
P:R

cyclin dependent kinase 6

17RAD50
RefP:G
17LMNB2
P:G

lamin B2

17KNL1
P:G

kinetochore scaffold 1

17MFSD2A
P:G

MFSD2 lysolipid transporter A, lysophospholipid

17ERCC5
DefP:A
17TRMT10A
P:G
17SMARCA4
Def#6

Microcephaly

17STAMBP
P:G

Progressive microcephaly

16AP4M1
DefP:A
16SASS6
P:G

SAS-6 centriolar assembly protein

16SMARCA5
ModP:G

SNF2 related chromatin remodeling ATPase 5

16NARS1
Mod
16CSNK2A1
DefP:G

Microcephaly

16GPT2
DefP:G

Microcephaly

16WDR11
P:G

WD repeat domain 11

15EHMT1
Def

Microcephaly

15ARF3
P:G

ARF GTPase 3

15CENPF
P:G
15FANCE
DefP:G

Microcephaly

15GRIN2B
Def
15NSD2
DefP:G
14CDKL5
Def
14NSD1
Def
14COPB2
P:R

Microcephaly

14PPP2R1A
Def
14MED17
P:A
14KAT6A
Def

Microcephaly

14TNPO2
P:G

transportin 2

14NUP37

nucleoporin 37

13CLASP1

cytoplasmic linker associated protein 1

13BRD4
DefP:A
13DNMT3A
DefP:G
13MCLMR

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

13MCPH2

MICROCEPHALY 2, PRIMARY, AUTOSOMAL RECESSIVE, WITH OR WITHOUT CORTICAL MALFORMATIONS; MCPH2

13MCPH4

MICROCEPHALY 4, PRIMARY, AUTOSOMAL RECESSIVE; MCPH4

13MICPCH

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

13MMACHC
Def
13MTHFR
Def
13MTRR
Def
13PHGDH
Def
13PRUNE1
P:G

Microcephaly

12PUS7
P:G
12SLF2
P:G
12SMC5
P:G
12TRAPPC12
P:G
12MVK
Def

Microcephaly

12MMADHC
Def
12MCM7
P:A

minichromosome maintenance complex component 7

12PRIM1
ModP:G

Microcephaly

11RARS2
Def

Microcephaly

11BCL11A
Def
11DNA2
ModP:G

Microcephaly

11RAB3GAP2
Def

Microcephaly

11AP4B1
DefP:A
11CRIPT
P:A
11WDFY3
DefP:R
11ACTG1
Def

Secondary microcephaly

11SLC4A10
StrP:G

Microcephaly

11TBCD
Def

Microcephaly

11ITPR1
Def

Microcephaly

10EIPR1
P:A
10KAT5

Microcephaly

10VPS50
P:A
10NCAPH
P:R

non-SMC condensin I complex subunit H

10BCOR
Def

Microcephaly

10GTPBP2
Def

Primary microcephaly

10AOPEP
10CZ1P-ASNS
10DONSON
P:G
10RAD51
P:G
10TMEM167A
P:G
10ACO2
Def

Microcephaly

10DYNC1I2
P:G

Microcephaly

9BCKDK
Def

Progressive microcephaly

9ADARB1
P:G

Microcephaly

9TUBGCP2
P:G

Progressive microcephaly

9DYNC1H1
Def
9FAM111A
Def
9KCNT1
Def
9SCN3A
Def
9SMARCA2
Def
9SOX11
Def
9ST3GAL5
Def
9UBE3B
Def
9SLC2A1
Def

Microcephaly

9CHD7
Def
9DDX41
Def
9MEIS2
Def
9TRAIP
P:G

Microcephaly

9PSAT1
Def

Microcephaly

9TCTN2
Def

Microcephaly

8GTF3C3
P:G

Microcephaly

8WDR4
P:G

Microcephaly

8GMNN
ModP:G

Microcephaly

8SNHG14

Possible

224 genes — click to expand
8TRAPPC14

trafficking protein particle complex subunit 14

8TRMT1
DefP:R

Microcephaly

7ANGPT2

angiopoietin 2

7NUS1
Def

Microcephaly

7PDHX
Def

Microcephaly

7COG6
Def

Microcephaly

7TELO2
Def

Microcephaly

7SLC35C1
Str

Microcephaly

7ABCC6
Def
7AFG3L2
Def
7B4GALT7
Def
7EPG5
Def
7F12
Def
7FOLR1
Def
7GABRB3
Def
7LMBRD1
Def
7MAGEL2
Def
7MPV17
Def
7MYH11
DefSF
7OCA2
Def
7POLH
Def
7SLC34A1
Def
7SMAD6
Def
7XPA
Def
7XPC
Def
7SLC6A8
Def

Microcephaly

7ZNF668
P:A

Microcephaly

7ATP9A
P:A

Secondary microcephaly

7CARS1

Microcephaly

7CUL3
Def

Microcephaly

7PLP1
Def

Microcephaly

7ZBTB18
Def

Microcephaly

6PYCR1
Def

Microcephaly

6KATNB1
6TAF2
6ZNF276
6EBF3
Def

Microcephaly

6STAG2

Microcephaly

6HYLS1
Mod
6WDR73
P:G

Secondary microcephaly

6KMT2A
Def

Microcephaly

6B3GLCT
Def

Microcephaly

5FARS2
Def

Microcephaly

5FGF12
Def

Secondary microcephaly

5MFF
Mod

Secondary microcephaly

5RAP1B
Mod

Secondary microcephaly

5SARS1
Lim

Microcephaly

5SUOX
Def

Microcephaly

5TMEM165
Mod

Secondary microcephaly

5KANSL1
Def

Microcephaly

5TBC1D24
Def

Microcephaly

5PGAP3
Def

Microcephaly

5ADAR
Def

Microcephaly

5RPS19
Def

Microcephaly

5POLR2A
Def

Microcephaly

5ABCC1
Lim
5BCL9
Lim
5CDK16
Lim
5CHD1L
Lim
5KMT2C
Def

Microcephaly

5L1CAM
Def

Microcephaly

5MCPHA

MICROCEPHALY, AMISH TYPE; MCPHA

5NEDMISBA

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

5ROBO1
Lim
5SF3B4
Def

Microcephaly

5SHANK3
Def

Microcephaly

5WARS1
Lim
5XRCC2
Lim
5ZC4H2
Def

Microcephaly

5PARS2
Mod

Secondary microcephaly

5SPTBN1
Def

Microcephaly

5MED27
Def

Microcephaly

5SHMT2
Lim

Microcephaly

5DPAGT1
Def

Microcephaly

5NOTCH3
Def

Primary microcephaly

5POLD1
DefSF

Microcephaly

5ZIC1
Def

Microcephaly

5SPTAN1
Def

Microcephaly

4SCO2
Def

Microcephaly

4HSPG2
Def

Microcephaly

4NDUFS4
Def

Microcephaly

4POMT2
Def

Microcephaly

4SPEN
Def

Microcephaly

4SPR
Def

Microcephaly

4VPS33A
Def

Microcephaly

4ACP6
4ARL10
4ATP10A
4ATP10A-DT
4BCAS3
4BIVM-ERCC5
4BMERB1
4CDHR2
4CDK19
4CEP20
4CTBP1
4CYFIP1
4DBN1
4DENND5A
4DOK3
4EIF4E1B
4EMC10
4FAF2
4FAM153A
4FAM153B
4FAM193B
4FARSB
4FGFR4
4FMO5
Dis
4GABRA5
4GABRG3
4GJA5
Dis
4GJA8
4GOLGA6L1
4GOLGA6L2
4GOLGA6L26
4GOLGA8S
4GPHRB
4GPRIN1
4GRK6
4HERC2
4HIGD2A
4HK3
4KIAA1191
4LMAN2
4MARF1
4MED25
Dis
4MKRN3
4MPV17L
4MPV17L-BMERB1
4MXD3
4NBPF11
4NIPA1
4NIPA2
4NOMO1
4NOP16
4NPAP1
4NPIPA1
4NPIPA5
4NTAN1
4PDLIM7
4PDXDC1
4PFN3
4PLEKHG2
4PPIAL4G
4PRELID1
4PRKAB2
Dis
4PRR7
4PUS3
4PWAR1
4PWAR4
4PWAR5
4PWAR6
4PWARSN
4PWRN1
4PWRN2
4PWRN3
4PWRN4
4PYCR2
4RAB24
4RGS14
4RNF17
4RNF44
4RNVU1-1
4RNVU1-3
4RNVU1-7
4RNVU1-8
4RRN3
4RUSC2
ModP:R

Secondary microcephaly

4SEPSECS
4SIMC1
4SMPD4
4SNRPN
4SNURF
4TCP1
4TMED9
4TRE-TTC2-2
4TRH-GTG1-2
4TRH-GTG1-3
4TRH-GTG1-4
4TRN-GTT9-2
4TRQ-CTG3-2
4TRQ-CTG4-1
4TRQ-CTG7-1
4TSPAN17
4TUBGCP5
4UIMC1
4UNC5A
4YWHAE
4ZNF346
4CBL
Def

Microcephaly

4PLPBP

Secondary microcephaly

4CACNA1G
Def

Microcephaly

4RARS1
Def

Microcephaly

4TECPR2

Microcephaly

4HCN1
Def

Microcephaly

4IFIH1
Def

Primary microcephaly

4ATP5PO
Str

Secondary microcephaly

4SIX3

Microcephaly

4SATB1
Def

Secondary microcephaly

4AFF3

Primary microcephaly

4TUBB3
Def

Microcephaly

4TET3
Def

Microcephaly

3MBTPS2
Def

Microcephaly

3STT3A
Def

Microcephaly

3CLCN3

Microcephaly

3CRELD1
Lim

Microcephaly

3GFM1
Mod

Microcephaly

3ACTL6B

Microcephaly

3GLI2

Microcephaly

3DOT1L

Microcephaly

3ACADSB
Def

Microcephaly

3COQ9
Def

Secondary microcephaly

3CPT2
Def

Microcephaly

3CYB5R3
Def

Microcephaly

3DGUOK
Def

Microcephaly

3DLD
Def

Microcephaly

3GNPAT
Def

Microcephaly

3NANS
Def

Microcephaly

3POMGNT1
Def

Microcephaly

3POMT1
Def

Microcephaly

3PRKDC
Def

Microcephaly

3SAMHD1
Def

Microcephaly

3UBR1
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.