Genes associated with “lissencephaly”

Diagnostic yield calculator →
242 genes foundHPO: Lissencephaly
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

17 genes
1
39
score
ClinGen: DefinitiveP2G #15GTR ↑

Lissencephaly

Frequency
100%
n=6
P/LP Variants
140
OT Score
-
2
37
score
ClinGen: DefinitiveGTR ↑

Agyria

Frequency
-
P/LP Variants
30
OT Score
-
3
35
score
ClinGen: DefinitiveP2G #20GTR ↑

Lissencephaly

Frequency
50%
n=4
P/LP Variants
11
OT Score
-
4
35
score
P2G #2GTR ↑

Agyria

Frequency
-
P/LP Variants
52
OT Score
-
5
31
score
ClinGen: DefinitiveP2G #18GTR ↑

Pachygyria

Frequency
82%
n=11
P/LP Variants
8
OT Score
-
6
31
score
ClinGen: StrongGTR ↑

Lissencephaly

Frequency
100%
n=7
P/LP Variants
6
OT Score
-
7
30
score
ClinGen: DefinitiveGTR ↑

Posterior predominant subcortical band heterotopia

Frequency
69%
n=13
P/LP Variants
16
OT Score
-
8
30
score
ClinGen: StrongGTR ↑

Lissencephaly

Frequency
100%
n=12
P/LP Variants
3
OT Score
-
9
29
score
ClinGen: ModerateGTR ↑

Lissencephaly

Frequency
100%
n=9
P/LP Variants
36
OT Score
-
28TUBA1A
Def#14

Agyria

27TUBG1
Def

Pachygyria

26PIDD1
Def

Lissencephaly

25ARX
Def

Lissencephaly

24LAMB1
Mod

Type II lissencephaly

21POMT1
Def

Type II lissencephaly

21FKTN
Def#19

Agyria

20CDK5
Mod

Lissencephaly

Consider

111 genes
18TMTC3

Type II lissencephaly

17FOXG1
Def

Pachygyria

17NSDHL
Mod#1

Pachygyria

17CRADD
Def

Pachygyria

16KATNB1

Pachygyria

16LARGE1
Def

Type II lissencephaly

15CRPPA
Def

Type II lissencephaly

14POMT2
Def

Type II lissencephaly

14FIG4
Def#3

Pachygyria

14RTTN
Def

Lissencephaly

14YWHAE
13WDR81
#13
13CASP2

Pachygyria

13ABCC6
Def
13ASPA
Def
13CILD47

CILIARY DYSKINESIA, PRIMARY, 47, AND LISSENCEPHALY; CILD47

13LIS1

LISSENCEPHALY 1; LIS1

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

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

13MYH11
DefSF
13ASPM
Def
12SNAP29
#6

Pachygyria

12ACTG1
Def

Lissencephaly

12TUBB2B
Def

Pachygyria

12TUBB3
Def

Lissencephaly

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

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
9MYO1C
Dis
9NPIPA5
9PITPNA
9SLC43A2
9TRPV1
9B3GALNT2
Def

Type II lissencephaly

9KCNQ2
Def
9TIMM22
Lim
9FKRP
Def

Agyria

9NFIX
Def

Pachygyria

8PSAT1
Def

Lissencephaly

8NR0B1
8POLA1
Mod
8CASK
Def

Pachygyria

8TBR1
Def

Pachygyria

8TCTN2
Def

Pachygyria

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

Pachygyria

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

Possible

99 genes — click to expand
8CTNNA2

Pachygyria

8B4GAT1
Mod

Type II lissencephaly

7ACTB
Def#16

Lissencephaly

7RPA1
Lim
7PIK3R2
Def

Pachygyria

7WDR62
Def

Lissencephaly

7ACSL4
Def
7ADGRG1
Def
7ALG13
Def
7HECW2
Def
7PAK3
Def
7PEX1
Def
7PEX5
Def
7SCN3A
Def
7ETFB
Def

Pachygyria

7RNU4ATAC
Def

Pachygyria

7DAG1
Def

Agyria

7POMGNT1
Def

Type II lissencephaly

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
6NTAN1
6OVCA2
6PDXDC1
6RRN3
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
6SETD1A
6ST3GAL3
Mod
6LMNB1
Def

Pachygyria

6ISCA1

Pachygyria

5GFM2
Mod

Pachygyria

5DCHS1
Mod

Pachygyria

5SLC26A5
Lim
5TPRKB

Pachygyria

5SLC30A9
Def

Pachygyria

5CAMSAP1

Lissencephaly

4CTU2

Lissencephaly

4TMX2

Lissencephaly

4KIF14

Microlissencephaly

4AMMECR1
4CCDC92B
4CUX1
4DNAJC2
4KCNN2
4MPV17L-BMERB1
4NOMO1
4NPIPA1
4NPIPA2
4NPIPA3
4NPIPA6
4NPIPA7
4P2RX1
Dis
4PCYT1B
4PLA2G10
4PMPCB
4RTL4
4RTL9
4TMEM164
4TRPC5
4TRPC5OS
4XYLT1
4TUBGCP2

Pachygyria

4GPX4

Focal lissencephaly

4WDR73

Pachygyria

4CCBE1

Pachygyria

3TCTN1

Pachygyria

3OSGEP

Pachygyria

3ZNHIT3

Pachygyria

3BLTP1
Def

Lissencephaly

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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.