Genes associated with “microcephaly”

Diagnostic yield calculator →
533 genes foundHPO: Microcephaly1 PanelApp panel
Some sources returned errors (1)

openTargets: Error: OT search: 403

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

44 genes
1
45
score
ClinGen: DefinitivePanel: Green ↑GTR ↑

Microcephaly

Frequency
100%
n=38
P/LP Variants
7
OT Score
-
2
43
score
ClinGen: DefinitivePanel: Green ↑GTR ↑
Frequency
-
P/LP Variants
11
OT Score
-
3
39
score
ClinGen: DefinitivePanel: Green ↑P2G #24GTR ↑

Progressive microcephaly

Frequency
100%
n=9
P/LP Variants
5
OT Score
-
4
37
score
ClinGen: DefinitivePanel: Green ↑P2G #22GTR ↑

Secondary microcephaly

Frequency
75%
n=16
P/LP Variants
2
OT Score
-
5
35
score
ClinGen: DefinitivePanel: Green ↑P2G #39GTR ↑
Frequency
-
P/LP Variants
7
OT Score
-
6
34
score
ClinGen: DefinitivePanel: Green ↑GTR ↑

Microcephaly

Frequency
-
P/LP Variants
4
OT Score
-
7
34
score
ClinGen: DefinitivePanel: Green ↑GTR ↑
Frequency
-
P/LP Variants
8
OT Score
-
8
34
score
ClinGen: DefinitivePanel: Green ↑GTR ↑
Frequency
-
P/LP Variants
7
OT Score
-
9
33
score
ClinGen: DefinitivePanel: Green ↑P2G #30GTR ↑
Frequency
-
P/LP Variants
1
OT Score
-
30TUBGCP6
DefP:G
30PNKP
DefP:G
30ZEB2
DefP:G
29ASNS
Def

Primary microcephaly

29MECP2
DefP:G
27NDE1
DefP:G
27LMNB1
DefP:G
26DHCR7
DefP:G#5
26EFTUD2
DefP:G

Progressive microcephaly

26TRIO
DefP:G
26FANCC
DefP:G
25FANCG
DefP:G
25FANCA
DefP:G
25TRAPPC6B
DefP:G

Progressive microcephaly

25PCNT
DefP:G
25ERCC4
DefP:G

Microcephaly

25CASK
DefP:G
25CTNNB1
DefP:G
25DYRK1A
DefP:G
25POGZ
DefP:G
25SLC1A4
DefP:G
25FANCI
DefP:G
25PALB2
DefSFP:A

Microcephaly

24CTCF
DefP:G
24SLC9A6
DefP:G
24HDAC8
DefP:G#15
24SMC1A
DefP:G#17
23ARFGEF2
Def

Microcephaly

23UBE3A
DefP:A
23MYCN
DefP:G

Microcephaly

22RAD21
DefP:G

Microcephaly

21SLX4
DefP:G
21ASXL1
Def
20ARCN1
P:A
20QARS1
Def

Consider

114 genes
20FANCD2
DefP:G
20PAH
Def
20TTI1
P:G

Microcephaly

20RAD51C
DefP:A
19FANCE
DefP:G
19RTTN
DefP:G
18TRMT10A
P:G
18AKT3
DefP:A
17RBBP8
P:G#12

Primary microcephaly

17RAD50
RefP:G
17DIAPH1
DefP:G
17ERCC5
DefP:A
17WDFY3
DefP:R
17CDK6
P:A

Primary microcephaly

17ORC4
ModP:G

Microcephaly

17STAMBP
P:G

Progressive microcephaly

16CENPF
P:G
16PPP2R1A
Def
16SOX11
Def

Microcephaly

15DNMT3A
DefP:G
15NARS1
Mod
15NCAPD2
P:G
15CEP57
DefP:G

Microcephaly

15PUS7
P:G

Microcephaly

15AP4M1
DefP:A
15ASXL3
Def
15GRIN2B
Def
15NSD2
DefP:G
14NSD1
Def
14BCL11A
Def
14SETD2
Def
14PHGDH
Def

Primary microcephaly

14PSAT1
Def

Microcephaly

14GPT2
DefP:G

Secondary microcephaly

13AP4B1
DefP:A
13BRD4
DefP:A
13DDX11
DefP:G
13MCLMR

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

13MCPH7

MICROCEPHALY 7, PRIMARY, AUTOSOMAL RECESSIVE; MCPH7

13MICPCH

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

13MMACHC
Def
13MTHFR
Def
13RNU4ATAC
DefP:G
13SMARCE1
Def#10

Microcephaly

13SPOUT1
P:G

Microcephaly

13ORC1
P:G

Microcephaly

13NSDHL
Mod
12CDKL5
Def
12ATP1A2
DefP:G

Microcephaly

12NCAPD3
P:G
12PCDH12
P:G
12PPFIBP1
P:G
12SLF2
P:G
12SMC5
P:G
12TRAPPC12
P:G
12MMADHC
Def
12UBE3B
Def
12PAFAH1B1
12TRAPPC9
DefP:G

Secondary microcephaly

12ESCO2
Def#14

Microcephaly

12WDR73
P:G

Microcephaly

12WDPCP
Def
11CRNKL1
P:G

Primary microcephaly

11CHD7
Def
11MEIS2
Def
11KATNB1

Microcephaly

11SCN3A
Def

Microcephaly

11CDC6
LimP:R

Microcephaly

11CRIPT
P:A
11MTRR
Def
11TUBG1
DefP:G

Microcephaly

11TAF2

Secondary microcephaly

11ATP6V0A2
Def

Progressive microcephaly

11PLK4
P:G

Microcephaly

10YIF1B
DefP:A

Microcephaly

10EIPR1
P:A
10MED17
P:A
10VPS50
P:A
10SLC38A3
P:G

Microcephaly

10UFC1
P:G

Secondary microcephaly

10BCOR
Def

Microcephaly

10ANKLE2
P:G
10AOPEP
10CEP135
P:G
10CZ1P-ASNS
10METTL5
P:G
10PRUNE1
P:G
10RAD51
P:G
10TMEM167A
P:G
10TOP3A
P:G
10UGP2
P:G
10KIF14
P:G

Microcephaly

10DYNC1H1
Def

Microcephaly

10ZNF526
P:G

Microcephaly

9TRA2B
DefP:A

Microcephaly

9TP53RK
P:G

Primary microcephaly

9ABCC6
Def
9EPG5
Def
9FAM111A
Def
9HIBCH
Def
9LMBRD1
Def
9MYH11
DefSF
9SMARCA2
Def
9ST3GAL5
Def
9HDAC4
9MKS1
Def

Microcephaly

9DDX41
Def
9KAT6A
Def
9SC5D

Microcephaly

9UGGT1
P:A

Secondary microcephaly

8GTF3C3
P:G

Microcephaly

8RAB3GAP1
Def

Microcephaly

8SMPD4
8SNHG14

Possible

331 genes — click to expand
8AP4S1
DefP:A

Microcephaly

8DENND5A

Microcephaly

8MSMO1
P:G

Microcephaly

8PTPN23
P:G

Microcephaly

8PTCH1
Def

Microcephaly

8NEXMIF
Def

Secondary microcephaly

7ABCC1
Lim
7AHDC1
Def

Microcephaly

7ANKRD17
Def

Microcephaly

7AFG2A
Def
7AFG3L2
Def
7AGXT
Def
7B4GALT7
Def
7BBS5
Def
7CACNA1D
Def
7CDK4
Def
7COL6A3
Def
7D2HGDH
Def
7F12
Def
7FOLR1
Def
7GABRB3
Def
7ITPR1
Def
7KCNT1
Def
7KIF1A
Def
7MAGEL2
Def
7MPV17
Def
7MTR
Def
7OCA2
Def
7OPN1LW
Def
7PEX13
Def
7POLH
Def
7SLC34A1
Def
7TBCD
Def
7THOC2
Def
7TUBA1A
Def
7XPA
Def
7EXOSC3

Progressive microcephaly

6FDXR
Def

Secondary microcephaly

6BMERB1
6CEP20
6EMC10
6MARF1
6MPV17L
6MPV17L-BMERB1
6NPIPA5
6NTAN1
6PDXDC1
6RNF14
6RRN3
6SEPSECS
6ZNF276
6MID1
Def

Microcephaly

6TNRC6B
Def

Microcephaly

6ADSL
Def

Microcephaly

6ATM
Def

Microcephaly

6HYLS1
Mod
6KLHL41
Mod
6MFSD2A
P:G

Progressive microcephaly

6NDUFA10
Mod
6REL
Mod
6RNU4-2
Str
6SUCLG1
Mod
6ATP11A
ModP:R

Microcephaly

6CTSD
Def

Microcephaly

6MICOS13
Def

Secondary microcephaly

5TRRAP
Def

Microcephaly

5FARS2
Def

Microcephaly

5IBA57
Def

Microcephaly

5EIF3F
Def

Microcephaly

5NOTCH3
Def

Microcephaly

5RPS19
Def

Microcephaly

5UNC13A
Def

Secondary microcephaly

5RFX7
Def

Microcephaly

5ARSL
Def

Microcephaly

5ARX
Def

Microcephaly

5BCL9
Lim
5CDK16
Lim
5CHD1L
Lim
5FGFR1
Def

Microcephaly

5MCPHA

MICROCEPHALY, AMISH TYPE; MCPHA

5MDH1

Progressive microcephaly

5NEDMISBA

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

5PDCD1
Lim
5PHF6
Def

Microcephaly

5ROBO1
Lim
5USP34
Lim
5WARS1
Lim
5XRCC2
Lim
5CEP63
P:R

Primary microcephaly

5SPTBN1
Def

Microcephaly

5ACBD5
Def

Progressive microcephaly

5ALG13
Def

Microcephaly

5COL18A1
Def

Microcephaly

5ENTPD1
Def

Microcephaly

5FOXRED1
Def

Secondary microcephaly

5GNPTAB
Def

Microcephaly

5IFT74
Def

Microcephaly

5OSTM1
Def

Microcephaly

5ZIC1
Def

Microcephaly

5IFIH1
Def

Microcephaly

5SPTAN1
Def

Microcephaly

5SNAP29

Progressive microcephaly

4COPB2
P:R

Microcephaly

4GFM2
Mod

Microcephaly

4PIGA
Def

Microcephaly

4DEGS1
Def

Secondary microcephaly

4KYNU
Def

Microcephaly

4SPR
Def

Microcephaly

4BRF1

Microcephaly

4ACKR3
4ACP6
4AGAP1
4ANKMY1
4ANO7
4AQP12A
4AQP12B
4ARL10
4ASB1
4ASB18
4ATG4B
4ATP10A
4ATP10A-DT
4B3GNT2
4BCAS3
4BIVM-ERCC5
4C2ORF74-DT
4CAPN10
4CAPN10-DT
4CARS1
4CCT4
4CDHR2
4CDK19
4CFAP210
4CLASP1
4COMMD1
4COPS8
4COPS8-DT
4COPS9
4CROCC2
4CTBP1
4CYFIP1
4DBN1
4DCLRE1B
4DEMA1
4DOK3
4DRC11
4DTYMK
4DUSP28
4EHBP1
4EIF4E1B
4ESPNL
4FAF2
4FAM153A
4FAM153B
4FAM161A
4FAM193B
4FAM240C
4FARP2
4FARSB
4FASTKD1
4FGFR4
4FMO5
Dis
4FSD1L
4GABRA5
4GABRG3
4GAL3ST2
4GBX2
4GJA5
Dis
4GJA8
4GOLGA6L1
4GOLGA6L2
4GOLGA6L26
4GOLGA8S
4GPC1
4GPHRB
4GPR35
4GPRIN1
4GRK6
4HDLBP
4HERC2
4HES6
4HIGD2A
4HK3
4IFT46
4IFT54
4ILKAP
4ING5
4KIAA1191
4KLHL23
4KLHL30
4LMAN2
4LRP2
No
4LRRC7
4LRRFIP1
4MAB21L4
4MED25
Dis
4MKRN3
4MTERF4
4MXD3
4MYCNOS
4NBPF11
4NEU4
4NIPA1
4NIPA2
4NOMO1
4NOMO3
4NOP16
4NPAP1
4NPIPA1
4NPIPA6
4NPIPA7
4OPSIN-LCR
4OR6B2
4OR6B3
4OTX1
4PAPOLG
4PDLIM7
4PELI1
4PER2
4PFN3
4PHOSPHO2
4PHOSPHO2-KLHL23
4PLEKHG2
4PPIAL4G
4PPP1R7
4PRELID1
4PRKAB2
Dis
4PRR21
4PRR7
4PUS10
4PUS3
4PWAR1
4PWAR4
4PWAR5
4PWAR6
4PWARSN
4PWRN1
4PWRN2
4PWRN3
4PWRN4
4PYCR2
4RAB17
4RAB17-DT
4RAB24
4RAMP1
4RBM44
4REL-DT
4RGS14
4RNF13
4RNF17
4RNF44
4RNPEPL1
4RNVU1-1
4RNVU1-3
4RNVU1-7
4RNVU1-8
4RTP5
4SANBR
4SEPTIN2
4SIMC1
4SIRT4
4SNED1
4SNORA70B
4SNRPN
4SNURF
4STK25
4TANAR
4TCP1
4THAP4
4TMED9
4TMEM17
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
4TWIST2
4UBE2F
4UBE2F-SCLY
4UBR3
4UICLM
4UIMC1
4UNC5A
4USP34-DT
4VPS54
4XPO1
4ZNF346
4ASPA
Def

Microcephaly

4GRIN2A
Def

Primary microcephaly

4RFT1
Mod

Microcephaly

4PLPBP

Secondary microcephaly

4CACNA1G
Def

Microcephaly

4ELAC2
Def

Microcephaly

4HIVEP2

Secondary microcephaly

4MAP1B
Str

Microcephaly

4NDUFA8
Mod

Microcephaly

4TOP2B
Mod

Primary microcephaly

4POLR3B
Def

Microcephaly

4PET100
Def

Microcephaly

3JARID2
Def

Microcephaly

3KDM6B
Def

Microcephaly

3TASP1

Microcephaly

3SRCAP
Def

Microcephaly

3GALNT2
Str

Microcephaly

3HMGCL
Def

Microcephaly

3BUD13

Microcephaly

3MDGA2

Secondary microcephaly

3BRAT1
Def

Microcephaly

3HUWE1
Def

Microcephaly

3ITGA3
Def

Microcephaly

3MOCS1
Def

Microcephaly

3MRPS22
Def

Microcephaly

3MYSM1
Def

Microcephaly

3NANS
Def

Microcephaly

3POMT1
Def

Microcephaly

3PUS1
Def

Microcephaly

3RNASEH2C
Def

Progressive microcephaly

3RNF168
Def

Microcephaly

3SALL1
Def

Microcephaly

3SET
Def

Microcephaly

3TBC1D24
Def

Secondary microcephaly

3TDP2
Def

Microcephaly

3TLK2
Def

Microcephaly

3TUSC3
Def

Microcephaly

3VARS2
Def

Microcephaly

3WWOX
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.