Genes associated with “lissencephaly”

Diagnostic yield calculator →
260 genes foundHPO: LissencephalyOpen Targets: lissencephaly spectrum disorders
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

25 genes
1
RELN →

reelin

52
score
ClinGen: DefinitiveP2G #15GTR ↑

Lissencephaly

Frequency
100%
n=6
P/LP Variants
133
OT Score
0.81
2
DCX →

doublecortin

52
score
ClinGen: DefinitiveGTR ↑

Agyria

Frequency
-
P/LP Variants
38
OT Score
0.87
3
PAFAH1B1 →

platelet activating factor acetylhydrolase 1b regulatory subunit 1

49
score
P2G #2GTR ↑

Subcortical band heterotopia

Frequency
-
P/LP Variants
55
OT Score
0.85
4
NDE1 →

nudE neurodevelopment protein 1

48
score
ClinGen: DefinitiveP2G #20GTR ↑

Lissencephaly

Frequency
50%
n=4
P/LP Variants
11
OT Score
0.80
5
CEP85L →

centrosomal protein 85L

43
score
ClinGen: DefinitiveGTR ↑

Posterior predominant subcortical band heterotopia

Frequency
69%
n=13
P/LP Variants
12
OT Score
0.79
6
MACF1 →

microtubule actin crosslinking factor 1

42
score
ClinGen: ModerateGTR ↑

Pachygyria

Frequency
100%
n=9
P/LP Variants
35
OT Score
0.81
7
ARX →

aristaless related homeobox

42
score
ClinGen: DefinitiveGTR ↑

Lissencephaly

Frequency
-
P/LP Variants
18
OT Score
0.81
8
TUBA1A →

tubulin alpha 1a

42
score
ClinGen: DefinitiveP2G #14GTR ↑

Agyria

Frequency
50%
n=8
P/LP Variants
54
OT Score
0.83
9
DYNC1H1 →

dynein cytoplasmic 1 heavy chain 1

38
score
ClinGen: DefinitiveP2G #18GTR ↑

Pachygyria

Frequency
82%
n=11
P/LP Variants
8
OT Score
0.43
38APC2
Str

Lissencephaly

37LAMB1
Mod

Type II lissencephaly

36PIDD1
Def

Lissencephaly

35TUBG1
Def

Pachygyria

34ACTG1
Def

Lissencephaly

33ACTB
Def#16

Pachygyria

32CDK5
Mod

Lissencephaly

31TP73
Str

Lissencephaly

30TMTC3

Type II lissencephaly

28KATNB1

Pachygyria

28POMT2
Def

Type II lissencephaly

28FKTN
Def#19

Type II lissencephaly

27FOXG1
Def

Pachygyria

22PSAT1
Def

Lissencephaly

21POMT1
Def

Agyria

21MYH11
DefSF

myosin heavy chain 11

Consider

117 genes
20PHGDH
Def

Lissencephaly

20WDR81
#13

WD repeat domain 81

19ASPM
Def

assembly factor for spindle microtubules

19CASP2
Mod

Pachygyria

19RAB3GAP1
Def

RAB3 GTPase activating protein catalytic subunit 1

18TUBB2B
Def

Lissencephaly

18RAB3GAP2
Def

RAB3 GTPase activating non-catalytic protein subunit 2

18RAB18
Mod

RAB18, member RAS oncogene family

17NSDHL
Mod#1

Pachygyria

17TUBB3
Def

Lissencephaly

17CRADD
Def

Pachygyria

16ADGRG1
Def

adhesion G protein-coupled receptor G1

16LARGE1
Def

Type II lissencephaly

15TBC1D20

TBC1 domain family member 20

14FIG4
Def#3

Pachygyria

14RTTN
Def

Lissencephaly

14YWHAE
13DAG1
Def

Agyria

13ABCC6
Def
13ASPA
Def
13CILD47

CILIARY DYSKINESIA, PRIMARY, 47, AND LISSENCEPHALY; CILD47

13LIS10

LISSENCEPHALY 10; LIS10

13LIS2

LISSENCEPHALY 2; LIS2

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

13MRT75

INTELLECTUAL DEVELOPMENTAL DISORDER, AUTOSOMAL RECESSIVE 75, WITH NEUROPSYCHIATRIC FEATURES AND VARIANT LISSENCEPHALY; MRT75

13MRT80

INTELLECTUAL DEVELOPMENTAL DISORDER, AUTOSOMAL RECESSIVE 80, WITH VARIANT LISSENCEPHALY; MRT80

12MYO1C
Dis

myosin IC

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
10PSPH
Mod

phosphoserine phosphatase

10ATP6V0A2
Def#8

Pachygyria

10CRPPA
Def

Type II lissencephaly

10POMGNT2
Def

Type II lissencephaly

10EML1
Def

Subcortical band heterotopia

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

Pachygyria

9CSNK2A1
Def

Pachygyria

9DPH1
Def
9INPP5K
9NPIPA5
9PITPNA
9SLC43A2
9TRPV1
9B3GALNT2
Def

Type II lissencephaly

9KCNQ2
Def
9TIMM22
Lim
9NFIX
Def

Pachygyria

8NR0B1
8POLA1
Mod
8CASK
Def

Pachygyria

8ZRANB3

zinc finger RANBP2-type containing 3

8TBR1
Def

Pachygyria

8FKRP
Def

Lissencephaly

8NBN
Def

nibrin

8TCTN2
Def

Pachygyria

8DOC2B
8EMC6
8GEMIN4
8GLOD4
8HASPIN
8ITGAE
8LIAT1
8MRM3
8NCBP3
8NTAN1
8P2RX5
8PDXDC1
8PEX2
Def

Pachygyria

8RFLNB
8RPH3AL
8RRN3
8SCARF1
8SERPINF1
8SGSM2
8SMG6
8SMYD4
8TAX1BP3
8TLCD2
8TLCD3A
8TSR1
8VPS53

Possible

102 genes — click to expand
8CTNNA2

Pachygyria

8B4GAT1
Mod

Type II lissencephaly

7RPA1
Lim
7SASS6
7PIK3R2
Def

Pachygyria

7WDR62
Def

Pachygyria

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

cathepsin D

7ETFB
Def

Pachygyria

7BAIAP2

Pachygyria

7RNU4ATAC
Def

Microlissencephaly

7POMGNT1
Def

Pachygyria

7MLYCD
Def

Pachygyria

7ETFA
Def

Pachygyria

7RMND1
Def

Pachygyria

7PRKDC
Def

Pachygyria

6KIFC3

kinesin family member C3

6TCTN1
Def

Pachygyria

6TUBGCP6
Def

Pachygyria

6CAMKK1
6CAPN6
6DCAF8L1
6DCAF8L2
6FTHL17
6MAGEB1
6MAGEB10
6MAGEB18
6MAGEB2
6MAGEB3
6MAGEB4
6MAGEB5
6MAGEB6
6MPV17L-BMERB1
6NPIPA6
6NPIPA7
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

Lissencephaly

6PSMC2
6CHRDL1
6SETD1A
6ST3GAL3
Mod
6LMNB1
Def

Pachygyria

6ISCA1

Pachygyria

5GFM2
Mod

Pachygyria

5DCHS1
Mod

Pachygyria

5EXOSC3

exosome component 3

5LIS1

LISSENCEPHALY 1; LIS1

5SLC26A5
Lim
5PLN
DefSF

phospholamban

5TPRKB

Pachygyria

5SLC30A9
Def

Pachygyria

5CAMSAP1

Pachygyria

4CTU2

Lissencephaly

4TMX2

Lissencephaly

4KIF14

Microlissencephaly

4AMMECR1
4CUX1
4DNAJC2
4KCNN2
4NOMO1
4NOMO2
4NPIPA1
4NPIPA2
4NPIPA3
4NPIPA8
4NPIPA9
4P2RX1
Dis
4PCYT1B
4PLA2G10
4PMPCB
4RTL4
4RTL9
4TMEM164
4TRPC5
4TRPC5OS
4XYLT1
4TUBA3E

tubulin alpha 3e

4TUBGCP2

Pachygyria

4GPX4

Focal lissencephaly

4WDR73

Pachygyria

4CCBE1

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.