Genes associated with “lissencephaly”

Diagnostic yield calculator →
261 genes foundHPO: LissencephalyOpen Targets: Lissencephaly
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
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Strong Candidates

20 genes
1
RELN →

reelin

47
score
ClinGen: DefinitiveP2G #15GTR ↑

Lissencephaly

Frequency
100%
n=6
P/LP Variants
141
OT Score
0.49
2
DCX →

doublecortin

45
score
ClinGen: DefinitiveGTR ↑

Pachygyria

Frequency
-
P/LP Variants
29
OT Score
0.46
3
PAFAH1B1 →

platelet activating factor acetylhydrolase 1b regulatory subunit 1

43
score
P2G #2GTR ↑

Pachygyria

Frequency
-
P/LP Variants
52
OT Score
0.50
4
NDE1 →

nudE neurodevelopment protein 1

42
score
ClinGen: DefinitiveP2G #20GTR ↑

Lissencephaly

Frequency
50%
n=4
P/LP Variants
10
OT Score
0.38
5
MACF1 →

microtubule actin crosslinking factor 1

39
score
ClinGen: ModerateGTR ↑

Pachygyria

Frequency
100%
n=9
P/LP Variants
34
OT Score
0.57
6
CEP85L →

centrosomal protein 85L

38
score
ClinGen: DefinitiveGTR ↑

Posterior predominant subcortical band heterotopia

Frequency
69%
n=13
P/LP Variants
17
OT Score
0.47
7
DYNC1H1 →

dynein cytoplasmic 1 heavy chain 1

38
score
ClinGen: DefinitiveP2G #18GTR ↑

Pachygyria

Frequency
82%
n=11
P/LP Variants
8
OT Score
0.41
8
TUBA1A →

tubulin alpha 1a

36
score
ClinGen: DefinitiveP2G #14GTR ↑

Agyria

Frequency
50%
n=8
P/LP Variants
58
OT Score
0.48
9
PIDD1 →

p53-induced death domain protein 1

36
score
ClinGen: DefinitiveGTR ↑

Pachygyria

Frequency
8%
n=12
P/LP Variants
22
OT Score
0.56
33TUBG1
Def

Pachygyria

31TP73
Str

Lissencephaly

30APC2
Str

Lissencephaly

28FKTN
Def#19

Type II lissencephaly

27FOXG1
Def

Pachygyria

26TMTC3

Type II lissencephaly

25ARX
Def

Lissencephaly

25KATNB1

Pachygyria

24LAMB1
Mod

Type II lissencephaly

21POMT2
Def

Type II lissencephaly

20CDK5
Mod

Lissencephaly

Consider

110 genes
19ASPM
Def

assembly factor for spindle microtubules

18TUBB2B
Def

Lissencephaly

18ACTG1
Def

Lissencephaly

17NSDHL
Mod#1

Pachygyria

17TUBB3
Def

Lissencephaly

17CRADD
Def

Lissencephaly

16FKRP
Def

Type II lissencephaly

16LARGE1
Def

Type II lissencephaly

15CRPPA
Def

Type II lissencephaly

14POMT1
Def

Agyria

14FIG4
Def#3

Pachygyria

14RTTN
Def

Lissencephaly

14YWHAE
13WDR81
#13
13CASP2

Pachygyria

13ADGRG1
Def

adhesion G protein-coupled receptor G1

13ABCC6
Def
13ASPA
Def
13CILD47

CILIARY DYSKINESIA, PRIMARY, 47, AND LISSENCEPHALY; CILD47

13LIS1

LISSENCEPHALY 1; LIS1

13LIS10

LISSENCEPHALY 10; LIS10

13LIS2

LISSENCEPHALY 2; LIS2

13LIS3

LISSENCEPHALY 3; LIS3

13LIS4

LISSENCEPHALY 4 WITH MICROCEPHALY; LIS4

13LIS6

LISSENCEPHALY 6 WITH MICROCEPHALY; LIS6

13LIS7

LISSENCEPHALY 7 WITH CEREBELLAR HYPOPLASIA; LIS7

13LIS8

LISSENCEPHALY 8; LIS8

13LIS9

LISSENCEPHALY 9 WITH COMPLEX BRAINSTEM MALFORMATION; LIS9

13LISX1

LISSENCEPHALY, X-LINKED, 1; LISX1

13LISX2

LISSENCEPHALY, X-LINKED, 2; LISX2

13MRT34

INTELLECTUAL DEVELOPMENTAL DISORDER, AUTOSOMAL RECESSIVE 34, WITH VARIANT LISSENCEPHALY; MRT34

13MYH11
DefSF
12EML1
Def

Subcortical band heterotopia

12SNAP29
#6

Pachygyria

12LAMC3
Dis

Pachygyria

11VLDLR
Def#5

Pachygyria

11DMD
Def
11IL1RAPL1
Def
11RXYLT1
Def

Type II lissencephaly

11ABCC1
Lim
11CTNS
Def
11PRPF8
Def
11SERPINF2
Def
10ATP6V0A2
Def#8

Pachygyria

10NFIX
Def

Pachygyria

10POMGNT2
Def

Type II lissencephaly

10TIMM22
Lim
10BHLHA9
10BMERB1
10CEP20
10INPP5K
10MARF1
10METTL16
10MPV17L
10MYO1C
Dis
10NOMO3
10OR1A1
10OR1A2
10OR1D2
10OR1D5
10OR1E1
10OR1E2
10OR1G1
10OR3A1
10OR3A2
10OR3A3
10PITPNA
10RAP1GAP2
10SPATA22
10TRARG1
10TRPV3
9HIC1
9ARHGAP31
#4

Pachygyria

9CSNK2A1
Def

Pachygyria

9DPH1
Def
9DOC2B
9GEMIN4
9GLOD4
9LIAT1
9MRM3
9RFLNB
9RPH3AL
9SLC43A2
9TLCD3A
9TRPV1
9VPS53
9B3GALNT2
Def

Type II lissencephaly

9KCNQ2
Def
8PSAT1
Def

Lissencephaly

8NR0B1
8POLA1
Mod
8CASK
Def

Pachygyria

8TBR1
Def

Pachygyria

8NBN
Def

nibrin

8TCTN2
Def

Pachygyria

8EMC6
8HASPIN
8ITGAE
8NCBP3
8NPIPA5
8P2RX5
8PEX2
Def

Pachygyria

8SCARF1
8SERPINF1
8SGSM2
8SMG6
8SMYD4
8TAX1BP3
8TLCD2
8TSR1

Possible

107 genes — click to expand
8CTNNA2

Pachygyria

8B4GAT1
Mod

Type II lissencephaly

7ACTB
Def#16

Pachygyria

7RPA1
Lim
7PIK3R2
Def

Pachygyria

7WDR62
Def

Pachygyria

7ACSL4
Def
7ALG13
Def
7HECW2
Def
7PAK3
Def
7PEX1
Def
7PEX5
Def
7SCN3A
Def
7ETFB
Def

Pachygyria

7RNU4ATAC
Def

Microlissencephaly

7DAG1
Def

Agyria

7POMGNT1
Def

Pachygyria

7MLYCD
Def

Pachygyria

7ETFA
Def

Pachygyria

7RMND1
Def

Pachygyria

7PHGDH
Def

Lissencephaly

7PRKDC
Def

Pachygyria

6TUBGCP6
Def

Pachygyria

6CAMKK1
6CAPN6
6DCAF8L1
6DCAF8L2
6FTHL17
6MAGEB1
6MAGEB10
6MAGEB18
6MAGEB2
6MAGEB3
6MAGEB4
6MAGEB5
6MAGEB6
6OVCA2
6RTN4RL1
6TAB3
6ETFDH
Def

Pachygyria

6VIPAS39
Def

Lissencephaly

6FAT4
Def

Subcortical band heterotopia

6KAT6B
Def

Pachygyria

6PEX10
Def

Pachygyria

6PEX13
Def

Lissencephaly

6KIF2A

Pachygyria

6KIFBP
Def

Pachygyria

6NEK1
Def

Pachygyria

6VPS33B
Def

Lissencephaly

6CCDC88A

Pachygyria

6PSMC2
6CHRDL1
6GLI3
Def

GLI family zinc finger 3

6SETD1A
6ST3GAL3
Mod
6L1CAM
Def

L1 cell adhesion molecule

6CHD7
Def

chromodomain helicase DNA binding protein 7

6LMNB1
Def

Pachygyria

6BAIAP2

Agyria

6ISCA1

Pachygyria

5GFM2
Mod

Pachygyria

5DCHS1
Mod

Pachygyria

5EXOSC3

exosome component 3

5SLC26A5
Lim
5TPRKB

Pachygyria

5SLC30A9
Def

Pachygyria

5CAMSAP1

Pachygyria

4CTU2

Lissencephaly

4TMX2

Lissencephaly

4KIF14

Microlissencephaly

4AMMECR1
4CCDC92B
4CUX1
4DNAJC2
4KCNN2
4NOMO1
4NPIPA1
4NPIPA2
4NPIPA3
4NTAN1
4P2RX1
Dis
4PCYT1B
4PDXDC1
4PLA2G10
4PMPCB
4RRN3
4RTL4
4RTL9
4TMEM164
4TRPC5
4TRPC5OS
4XYLT1
4ALX1
Def

ALX homeobox 1

4TUBA3E

tubulin alpha 3e

4FGFR2
Def

fibroblast growth factor receptor 2

4FOXC1
Def

forkhead box C1

4MAPK8IP3
Def

mitogen-activated protein kinase 8 interacting protein 3

4TUBGCP2

Pachygyria

4FGFR3
Def

fibroblast growth factor receptor 3

4HTT
Def

huntingtin

4GPX4

Focal lissencephaly

4WDR73

Pachygyria

4CCBE1

Pachygyria

3TCTN1

Pachygyria

3OSGEP

Lissencephaly

3ZNHIT3

Pachygyria

3BLTP1
Def

Lissencephaly

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.