Genes associated with “megalencephaly”

521 genes foundHPO: MegalencephalyOpen Targets: megalencephaly505 ClinVar P/LP variants
Some sources returned errors (2)

omim: Error: OMIM search: 429

omimClinSyn: Error: OMIM CS: 429

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

8 genes
1
PIK3CA →

phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha

34
score
ClinGen: DefinitiveP2G #4GTR ↑

megalencephaly-capillary malformation-polymicrogyria syndrome

Frequency
-
P/LP Variants
110
OT Score
0.34
2
28
score
ClinGen: DefinitiveP2G #6GTR ↑

megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2

Frequency
100%
n=20
P/LP Variants
21
OT Score
-
3
27
score
ClinGen: DefinitiveP2G #2GTR ↑

severe achondroplasia-developmental delay-acanthosis nigricans syndrome

Frequency
25%
n=4
P/LP Variants
35
OT Score
-
4
26
score
ClinGen: DefinitiveP2G #13GTR ↑

megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 3

Frequency
100%
n=12
P/LP Variants
15
OT Score
-
5
26
score
ClinGen: DefinitiveP2G #1GTR ↑
Frequency
-
P/LP Variants
178
OT Score
-
6
25
score
ClinGen: DefinitiveP2G #9GTR ↑

macrocephaly-intellectual disability-neurodevelopmental disorder-small thorax syndrome

Frequency
25%
n=4
P/LP Variants
5
OT Score
-
7
PTEN →

phosphatase and tensin homolog

25
score
ClinGen: DefinitiveACMG SFP2G #14GTR ↑

Cowden syndrome 1

Frequency
-
P/LP Variants
6
OT Score
0.37
8
TBC1D7 →

TBC1 domain family member 7

22
score
P2G #18GTR ↑

macrocephaly/megalencephaly syndrome, autosomal recessive

Frequency
-
P/LP Variants
3
OT Score
0.65

Consider

25 genes
17HRAS
DefSF#7

linear nevus sebaceous syndrome

17PIK3R2
Def#8

megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 1

16PIK3R1
Def
16NRAS
Def#5

linear nevus sebaceous syndrome

15HERC1
#19

macrocephaly, dysmorphic facies, and psychomotor retardation

14STRADA
#17

polyhydramnios, megalencephaly, and symptomatic epilepsy

13KPTN
Def
12LRRC56
Mod
12HEPACAM
Def

megalencephalic leukoencephalopathy with subcortical cysts 1

11SDCCAG8
Def
11FGFR2
Def#3

Apert syndrome

11TSC2
DefSF#11

tuberous sclerosis 2

11KRAS
Def#12

linear nevus sebaceous syndrome

10CEP170
10RNASET2
9CREBBP
Def
9FOXP1
Def
9PKD1
Def
9PTCH1
Def
9PTPN11
Def
9SCN2A
Def
9ZBTB18
Def
9CD19
Def
9KATNIP
Def

katanin interacting protein

8TBC1D7-LOC100130357

Possible

461 genes — click to expand
7L1CAM
Def

L1 cell adhesion molecule

7RAB39B
Def

early-onset parkinsonism-intellectual disability syndrome

7SMO
Def#16

Curry-Jones syndrome

7ABCA3
Def
7ABCC6
Def
7ACTN2
Def
7ALG1
Def
7ARL6IP1
Def
7B3GALNT2
Def
7BCKDK
Def
7BRAF
Def
7CIITA
Def
7CLCN7
Def
7CLN3
Def
7COA6
Def
7COG7
Def
7COL7A1
Def
7CORO1A
Def
7EARS2
Def
7EGLN1
Def
7ERCC4
Def
7FUS
Def
7GFER
Def
7GNPAT
Def
7GNPTG
Def
7GRIN2A
Def
7HSD3B7
Def
7IFT140
Def
7IL21R
Def
7KMT5B
Def
7LAT
Def
7LYST
Def
7MAPK8IP3
Def
7MEFV
Def
7MTR
Def
7MYH11
DefSF
7NDE1
Def
7NTHL1
Def
7OTOA
Def
7PALB2
DefSF
7PARN
Def
7PHKG2
Def
7PMM2
Def
7PRRT2
Def
7RIT1
Def
7ROGDI
Def
7RYR2
DefSF
7SCNN1G
Def
7SLX4
Def
7SOCS1
Def
7SRCAP
Def
7STX1B
Def
7TBC1D24
Def
7TELO2
Def
7THOC6
Def
7TRAF7
Def
7UMOD
Def
7USP7
Def
7MLC1
Def

megalencephalic leukoencephalopathy with subcortical cysts 1

6MYCNOS
6PLD5
6ABAT
Mod
6COX6A2
Mod
6GALNT2
Str
6GLIS2
Mod
6LITAF
Mod
6MRPS34
Mod
6NDUFB10
Mod
6RPL3L
Mod
6SETD1A
6SPTBN1
Str
6SRRM2
6TBCE
Mod
6TUFM
Mod
6UQCRC2
Mod
6VKORC1
Mod
6KIF6

kinesin family member 6

6SMARCB1
Def

SWI/SNF related BAF chromatin remodeling complex subunit B1

6ITGAM
6TSC1
DefSF#10

tuberous sclerosis 1

6ITGAX
6EIF2B5
Def

leukoencephalopathy with vanishing white matter 5

6ITGAD
5DEPDC5
Def#20

epilepsy, familial focal, with variable foci 1

5CRADD
Def

intellectual disability, autosomal recessive 34

5ABCC1
Lim
5CCNF
Lim
5COG2
Lim
5CRYM
Lim
5CTF1
Lim
5DNASE1
Lim
5GREM2
Lim
5IRF2BP2
Lim
5RNF40
Lim
5PEX6
Def

peroxisomal biogenesis factor 6

4ACSM1
4ACSM2A
4ACSM2B
4ACSM3
4ACSM5
4ADCY9
4AKT3-IT1
4ALDOA
4AMDHD2
4ANKS3
4ANKS4B
4APOBR
4AQP8
4ARHGAP17
4ARID4B
4ARMC5
4ARV1
4ASPHD1
4ATF7IP2
4ATP2A1
4ATP6V0C
4ATXN2L
4BAIAP3
4BCAR4
4BCL7C
4BECN2
4BICDL2
4BMERB1
4BOLA2
4BOLA2B
4BRICD5
4C16ORF54
4C16ORF82
4C16ORF89
4C16ORF90
4C16ORF92
4C16ORF96
4C1ORF198
4CACNG3
4CAPN9
4CARHSP1
4CASKIN1
4CCDC154
4CCP110
4CD2BP2
4CDIP1
4CDIPT
4CDR2
4CEMP1
4CEP20
4CFAP119
4CHP2
4CHRM3
4CLDN6
4CLDN9
4CLEC16A
4CLEC19A
4CLUAP1
4COQ7
4CORO7
4CORO7-PAM16
4CPPED1
4CRAMP1
4DCTN5
4DCTPP1
4DCUN1D3
4DISC1
4DISC1-IT1
4DISC2
4DNAAF8
4DNAH3
4DNAJA3
4DNASE1L2
4DOC2A
4E4F1
4ECI1
4EDARADD
4EEF2K
4EEF2KMT
4EIF3C
4EIF3CL
4EME2
4EMP2
4ERI2
4ERN2
4ERO1B
4EXO1
Ref
4EXOC8
4FAHD1
4FAM89A
4FBXL19
4FLYWCH1
4FLYWCH2
4FMN2
4FSAF1
4GDE1
4GDPD3
4GGA2
4GGPS1
4GLYR1
4GNA11
4GNG4
4GP2
4GPR137B
4GPR139
4GPRC5B
4GSG1L
4GSPT1
4GTF3C1
4HAPSTR1
4HCFC1R1
4HEATR1
4HIRIP3
4HMOX2
4HS3ST2
4HS3ST4
4HS3ST6
4IGFALS
4IGSF6
4IL27
4IL32
4IL4R
4INO80E
4ITGAL
4ITPRIPL2
4JPT2
4KAT8
4KCNK1
4KCNN2
4KCTD13
4KCTD5
4KDM8
4KIF22
4KMO
No
4KNOP1
4KRABD5
4KREMEN2
4LCMT1
4LDAF1
4LGALS8
4LMBRD2
4LNCATV
4LYRM1
4MAP10
4MAP1LC3C
4MAP3K21
4MAPK3
4MARF1
4MEIOB
4METTL22
4METTL9
4MGRN1
4MLST8
4MMP25
4MOSMO
4MPV17L
4MRTFB
4MSRB1
4MT1HL1
4MTRNR2L4
4MYL11
4NAA60
4NAGPA
4NDUFAB1
4NFATC2IP
4NHERF2
4NID1
4NLRC3
4NME3
4NMRAL1
4NOMO1
4NOMO2
4NOMO3
4NOXO1
4NPIPA1
4NPIPA2
4NPIPA3
4NPIPA5
4NPIPB3
4NPIPB4
4NPIPB5
4NPIPB6
4NSMCE1
4NTAN1
4NTN3
4NTPCR
4NUBP1
4NUBP2
4NUDT16L1
4NUPR1
4OPN3
4OR1F1
4OR2C1
4ORAI3
4PAGR1
4PAM16
4PAQR4
4PCNX2
4PDILT
4PDPK1
4PDXDC1
4PDZD9
4PGBD5
4PKMYT1
4PLA2G10
4PLK1
4POLR3E
4PPP2R5C
4PPP4C
4PRKCB
4PRM1
4PRM2
4PRM3
4PRR14
4PRSS21
4PRSS22
4PRSS27
4PRSS33
4PRSS36
4PRSS41
4PRSS53
4PRSS8
4PTX4
4PYCARD
4PYDC1
4RAB26
4RABEP2
4RBBP6
4RBFOX1
4RBM34
4RGS7
4RMI2
4RNF151
4RNPS1
4RPS15A
4RPS2
4RRN3
4RSL1D1
4RUSF1
4SBK1
4SCAMP5
4SCNN1B
4SDR42E2
4SEC14L5
4SEPHS2
4SEPTIN1
4SEPTIN12
4SEZ6L2
4SGF29
4SH2B1
4SHISA9
4SIPA1L2
4SLC35F3
4SLC5A11
4SLC5A2
4SLX1A
4SLX1B
4SMG1
4SMIM22
4SNHG9
4SNORA14B
4SNX29
4SPMIP3
4SPNS1
4SPRTN
4SPSB3
4STX4
4SULT1A1
4SULT1A2
4SULT1A3
4SULT1A4
4SYNGR3
4SYT17
4TAOK2
4TARBP1
4TBC1D10B
4TBL3
4TBX6
4TEDC2
4TEKT5
4TFAP4
4TGFB1I1
4THUMPD1
4TIGD7
4TLCD3B
4TMC5
4TMC7
4TMEM114
4TMEM186
4TMEM204
4TMEM219
4TNFRSF12A
4TNFRSF17
4TNP2
4TNRC6A
4TOMM20
4TP53TG3
4TP53TG3B
4TP53TG3C
4TP53TG3D
4TPSAB1
4TPSB2
4TPSD1
4TRAP1
4TRIM67
4TRIM72
4TSNAX
4TSNAX-DISC1
4TSNAX-DT
4TSR3
4TTC13
4TVP23A
4TXNDC11
4UBALD1
4UBE2I
4UBFD1
4UBN1
4UQCC4
4USP31
4VPS35L
4VWA3A
4WDR64
4XPO6
4XYLT1
4YPEL3
4ZC3H7A
4ZG16
4ZG16B
4ZKSCAN2
4ZNF174
4ZNF200
4ZNF205
4ZNF213
4ZNF263
4ZNF267
4ZNF48
4ZNF500
4ZNF597
4ZNF598
4ZNF629
4ZNF646
4ZNF668
4ZNF688
4ZNF689
4ZNF747
4ZNF75A
4ZNF764
4ZNF768
4ZNF771
4ZNF785
4ZNF843
4ZP2
4ZP4
4ZSCAN10
4ZSCAN32
4MYH10
Def

myosin heavy chain 10

4HNRNPH2
Def

heterogeneous nuclear ribonucleoprotein H2

4DRC4
Def

dynein regulatory complex subunit 4

4DNAI1
Def

dynein axonemal intermediate chain 1

4CCDC39
Def

coiled-coil domain 39 molecular ruler complex subunit

4DRC1
Def

dynein regulatory complex subunit 1

4FOXJ1
Def

forkhead box J1

4COL18A1
Def

collagen type XVIII alpha 1 chain

4MBOAT7
Def

membrane bound acylglycerophosphatidylinositol O-acyltransferase MBOAT7

3GLDC
Def

glycine decarboxylase

3PLCB1
Def

phospholipase C beta 1

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