Genes associated with “lissencephaly

245 genes foundHPO: LissencephalyOpen Targets: Lissencephaly1077 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:
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Strong Candidates

24 genes
1
RELN

reelin

47
score
ClinGen: DefinitiveP2G #15GTR ↑

Norman-Roberts syndrome

Frequency
100%
n=6
P/LP Variants
144
OT Score
0.48
2
DCX

doublecortin

45
score
ClinGen: DefinitiveGTR ↑

lissencephaly type 1 due to doublecortin gene mutation

Frequency
-
P/LP Variants
28
OT Score
0.46
3
PAFAH1B1

platelet activating factor acetylhydrolase 1b regulatory subunit 1

43
score
P2G #2GTR ↑

lissencephaly due to LIS1 mutation

Frequency
-
P/LP Variants
52
OT Score
0.49
4
NDE1

nudE neurodevelopment protein 1

42
score
ClinGen: DefinitiveP2G #20GTR ↑

lissencephaly 4

Frequency
50%
n=4
P/LP Variants
8
OT Score
0.37
5
MACF1

microtubule actin crosslinking factor 1

39
score
ClinGen: ModerateGTR ↑

lissencephaly 9 with complex brainstem malformation

Frequency
100%
n=9
P/LP Variants
32
OT Score
0.57
6
CEP85L

centrosomal protein 85L

38
score
ClinGen: DefinitiveGTR ↑

lissencephaly 10

Frequency
69%
n=13
P/LP Variants
20
OT Score
0.47
7
DYNC1H1

dynein cytoplasmic 1 heavy chain 1

38
score
ClinGen: DefinitiveP2G #18GTR ↑

intellectual disability, autosomal dominant 13

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

tubulin alpha 1a

38
score
ClinGen: DefinitiveP2G #14GTR ↑

lissencephaly due to TUBA1A mutation

Frequency
50%
n=8
P/LP Variants
55
OT Score
0.58
9
PIDD1

p53-induced death domain protein 1

36
score
ClinGen: DefinitiveGTR ↑

intellectual developmental disorder, autosomal recessive 75, with neuropsychiatric features and variant lissencephaly

Frequency
8%
n=12
P/LP Variants
19
OT Score
0.55
33LAMB1
Mod

cobblestone lissencephaly without muscular or ocular involvement

33TUBG1
Def

complex cortical dysplasia with other brain malformations 4

31APC2
Str

cortical dysplasia, complex, with other brain malformations 10

31TP73
Str

ciliary dyskinesia, primary, 47, and lissencephaly

lissencephaly 8

29ARX
Def

X-linked lissencephaly with abnormal genitalia

28FKTN
Def#19

muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A1

27ACTG1
Def

Baraitser-winter syndrome 2

26FOXG1
Def

FOXG1 disorder

25TUBB2B
Def

complex cortical dysplasia with other brain malformations 7

25FKRP
Def

muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A1

lissencephaly 6 with microcephaly

21POMT1
Def

muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A1

21POMT2
Def

muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A1

20CDK5
Mod

lissencephaly 7 with cerebellar hypoplasia

Consider

93 genes
19ASPM
Def

assembly factor for spindle microtubules

17NSDHL
Mod#1

CK syndrome

17CRADD
Def

intellectual disability, autosomal recessive 34

17TUBB3
Def

complex cortical dysplasia with other brain malformations 1

15CRPPA
Def

muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 7

14FIG4
Def#3

Yunis-Varon syndrome

14RTTN
Def

microcephalic primordial dwarfism due to RTTN deficiency

13WDR81
#13

intellectual developmental disorder, autosomal recessive 80, with variant lissencephaly

13ADGRG1
Def

adhesion G protein-coupled receptor G1

13ABCC6
Def
13ASPA
Def
13MYH11
DefSF
12SNAP29
#6

CEDNIK syndrome

12LAMC3
Dis

occipital pachygyria and polymicrogyria

11VLDLR
Def#5

cerebellar ataxia, intellectual disability, and dysequilibrium syndrome 1

11DMD
Def
11RXYLT1
Def

muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 10

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

autosomal recessive cutis laxa type 2A

10POMGNT2
Def

muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 8

10TIMM22
Lim
10EML1
Def

band heterotopia of brain

10MYO1C
Dis

Adams-Oliver syndrome 1

Okur-Chung neurodevelopmental syndrome

9DPH1
Def

muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 11

9KCNQ2
Def
9NFIX
Def

Marshall-Smith syndrome

9LARGE1
Def

muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A1

8PSAT1
Def

Neu-Laxova syndrome 2

8POLA1
Mod
8CASK
Def

syndromic X-linked intellectual disability Najm type

8TBR1
Def

intellectual developmental disorder with autism and speech delay

8NBN
Def

nibrin

8TCTN2
Def

Joubert syndrome 24

8PEX2
Def

peroxisome biogenesis disorder 5A (Zellweger)

Possible

102 genes — click to expand

cortical dysplasia, complex, with other brain malformations 9

8B4GAT1
Mod

muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13

7ACTB
Def#16

Baraitser-Winter syndrome 1

7RPA1
Lim
7PIK3R2
Def

megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 1

7WDR62
Def

microcephaly 2, primary, autosomal recessive, with or without cortical malformations

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

multiple acyl-CoA dehydrogenase deficiency

microcephalic osteodysplastic primordial dwarfism type I

7DAG1
Def

muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A9

muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A3

7MLYCD
Def

malonic aciduria

7ETFA
Def

multiple acyl-CoA dehydrogenase deficiency

7RMND1
Def

combined oxidative phosphorylation defect type 11

7PHGDH
Def

Neu-Laxova syndrome 1

7PRKDC
Def

severe combined immunodeficiency due to DNA-PKcs deficiency

microcephaly and chorioretinopathy 1

6ETFDH
Def

multiple acyl-CoA dehydrogenase deficiency

arthrogryposis, renal dysfunction, and cholestasis 2

6FAT4
Def

van Maldergem syndrome 2

6KAT6B
Def

genitopatellar syndrome

6PEX10
Def

peroxisome biogenesis disorder 6A (Zellweger)

6PEX13
Def

peroxisome biogenesis disorder 11A (Zellweger)

complex cortical dysplasia with other brain malformations 3

6KIFBP
Def

Goldberg-Shprintzen syndrome

6NEK1
Def

short-rib thoracic dysplasia 6 with or without polydactyly

6VPS33B
Def

arthrogryposis, renal dysfunction, and cholestasis 1

PEHO-like syndrome

6LMNB1
Def

microcephaly 26, primary, autosomal dominant

6LMX1B
Def

LIM homeobox transcription factor 1 beta

multiple mitochondrial dysfunctions syndrome 5

5GFM2
Mod

combined oxidative phosphorylation deficiency 39

5DCHS1
Mod

van Maldergem syndrome 1

exosome component 3

Galloway-Mowat syndrome 5

psychomotor regression-oculomotor apraxia-movement disorder-nephropathy syndrome

cortical dysplasia, complex, with other brain malformations 12

microcephaly, facial dysmorphism, renal agenesis, and ambiguous genitalia syndrome

neurodevelopmental disorder with microcephaly, cortical malformations, and spasticity

microcephaly 20, primary, autosomal recessive

tubulin alpha 3e

pachygyria, microcephaly, developmental delay, and dysmorphic facies, with or without seizures

spondylometaphyseal dysplasia, Sedaghatian type

4MYH10
Def

myosin heavy chain 10

Galloway-Mowat syndrome 1

Hennekam lymphangiectasia-lymphedema syndrome 1

4PXDN
Def

peroxidasin

SHH signaling and ciliogenesis regulator SDCCAG8

mitogen-activated protein kinase 8 interacting protein 3

3GNPAT
Def

glyceronephosphate O-acyltransferase

Joubert syndrome 13

Galloway-Mowat syndrome 3

PEHO syndrome

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