Lissencephaly, X-Linked, 2 (LISX2)

Categories: Endocrine diseases, Fetal diseases, Genetic diseases, Mental diseases, Neuronal diseases, Rare diseases, Reproductive diseases

Aliases & Classifications for Lissencephaly, X-Linked, 2

MalaCards integrated aliases for Lissencephaly, X-Linked, 2:

Name: Lissencephaly, X-Linked, 2 57 70
Hydranencephaly with Abnormal Genitalia 57 20 29 13 6
X-Linked Lissencephaly with Ambiguous Genitalia 12 20 43 58
X-Linked Lissencephaly with Abnormal Genitalia 12 20 43 58
Xlisg 57 20 43 72
Xlag 57 12 43 72
X-Linked Lissencephaly-Corpus Callosum Agenesis-Genital Anomalies Syndrome 12 20 58
Lissencephaly, X-Linked 2 57 20 72
Xlag Syndrome 12 20 58
Lisx2 57 43 72
Lissencephaly, X-Linked, with Ambiguous Genitalia 57 20
Lissencephaly 2, X-Linked 29 6
X-Linked Lissencephaly 2 12 43
X-Linked Lissencephaly-Agenesis of the Corpus Callosum-Genital Anomalies Syndrome 20
X-Linked Lissencephaly - Agenesis of the Corpus Callosum - Genital Anomalies 20
Lissencephaly, X-Linked, with Ambiguous Genitalia; Xlag 57
Lissencephaly X-Linked with Ambiguous Genitalia 72
Chromosome Xq26.3 Duplication Syndrome 70
Lissencephaly, X-Linked, Type 2 39
Xlag Syndrome 20
Xlis2 12


Orphanet epidemiological data:

x-linked lissencephaly with abnormal genitalia
Inheritance: X-linked recessive; Age of onset: Neonatal; Age of death: early childhood;


57 (Updated 05-Apr-2021)

early death in males
some female carriers are more mildly affected


lissencephaly, x-linked, 2:
Onset and clinical course death in infancy
Inheritance x-linked inheritance


Orphanet: 58  
Rare neurological diseases
Rare endocrine diseases
Developmental anomalies during embryogenesis

Summaries for Lissencephaly, X-Linked, 2

GARD : 20 The following summary is from Orphanet, a European reference portal for information on rare diseases and orphan drugs. Orpha Number: 452 Definition X-linked lissencephaly with abnormal genitalia (XLAG) is a rare, genetic, central nervous system malformation disorder characterized, in males, by lissencephaly (with posterior predominance and moderately thickened cortex), complete absence of corpus callosum, neonatal-onset (mainly perinatal) intractable seizures, postnatal microcephaly, severe hypotonia, poor responsiveness and hypogonadism (micropenis, hypospadias, cryptorchidism, small scrotal sac). Defective temperature regulation and chronic diarrhea may be additionally observed. Clinical description XLAG differs considerably from classical lissencephaly, as the resulting cortical thickness is only 6-7 mm in XLAG, rather than 15-20 mm seen in classical lissencephaly due to mutations of the PAFAH1B1 or DCX genes. Etiology In 2002, mutations in the X-linked aristaless-related homeobox gene ( ARX ; Xp21.3) were identified in individuals with XLAG and in some of their female relatives. Mouse Arx and human ARX are highly expressed in both dorsal and ventral telencephalon, including the neocortical ventricular zone and germinal zone of the ganglionic eminence, with less intense signals in the subventricular zone, cortical plate, hippocampus, basal ganglia and ventral thalamus. Arx-deficient mice showed deficient tangential migration and abnormal differentiation of GABAergic interneurons in the ganglionic eminence and neocortex, as well as abnormal testicular differentiation. These characteristics include some of the clinical features of XLAG in humans. The ARX mutations in XLAG patients were predominantly premature termination mutations (large deletions, frameshift, nonsense mutations, splice site mutations) while the missense mutations were less common and located essentially in the homeobox domain. Patients carrying nonconservative missense mutations within the homeobox, showed less severe XLAG, while conservative substitution in the homeodomain caused Proud syndrome (ACC with abnormal genitalia). A non conservative missense mutation near the C-terminal aristaless domain caused unusually severe XLAG with microcephaly and mild cerebellar hypoplasia. The ARX mutations are also associated with a spectrum of milder phenotypes, without macroscopic malformations of the brain, such as X-linked infantile spasms, a syndrome featuring mental retardation associated with distal dystonic movements (Partington syndrome; see this term), autistic features and nonsyndromicintellectual deficit.

MalaCards based summary : Lissencephaly, X-Linked, 2, also known as hydranencephaly with abnormal genitalia, is related to mental retardation, x-linked, with or without seizures, arx-related and partington x-linked mental retardation syndrome, and has symptoms including snoring and thick skin. An important gene associated with Lissencephaly, X-Linked, 2 is ARX (Aristaless Related Homeobox). Affiliated tissues include brain, testes and cortex, and related phenotypes are intellectual disability and agenesis of corpus callosum

Disease Ontology : 12 A lissencephaly characterized by structural brain anomalies, early-onset intractable seizures, severe psychomotor retardation, and ambiguous genitalia that has material basis in mutation in ARX on chromosome Xp21.3.

MedlinePlus Genetics : 43 X-linked lissencephaly with abnormal genitalia (XLAG) is a condition that affects the development of the brain and genitalia. It occurs most often in males.XLAG is characterized by abnormal brain development that results in the brain having a smooth appearance (lissencephaly) instead of its normal folds and grooves. Individuals without any folds in the brain (agyria) typically have more severe symptoms than people with reduced folds and grooves (pachygyria). Individuals with XLAG may also have a lack of development (agenesis) of the tissue connecting the left and right halves of the brain (corpus callosum). The brain abnormalities can cause severe intellectual disability and developmental delay, abnormal muscle stiffness (spasticity), weak muscle tone (hypotonia), and feeding difficulties. Starting soon after birth, babies with XLAG have frequent and recurrent seizures (epilepsy). Most children with XLAG do not survive past early childhood.Another key feature of XLAG in males is abnormal genitalia that can include an unusually small penis (micropenis), undescended testes (cryptorchidism), or external genitalia that do not look clearly male or clearly female (ambiguous genitalia).Additional signs and symptoms of XLAG include chronic diarrhea, periods of increased blood sugar (transient hyperglycemia), and problems with body temperature regulation.

OMIM® : 57 X-linked lissencephaly-2 (LISX2) is a developmental disorder characterized by structural brain anomalies, early-onset intractable seizures, severe psychomotor retardation, and ambiguous genitalia. Males are severely affected and often die within the first days or months of life, whereas females may be unaffected or have a milder phenotype (Bonneau et al., 2002). LISX2 is part of a phenotypic spectrum of disorders caused by mutation in the ARX gene comprising a nearly continuous series of developmental disorders ranging from hydranencephaly and lissencephaly to Proud syndrome (300004) to infantile spasms without brain malformations (DEE1; 308350) to syndromic (309510) and nonsyndromic (300419) mental retardation (Kato et al., 2004; Wallerstein et al., 2008). For a general phenotypic description and a discussion of genetic heterogeneity of lissencephaly, see LIS1 (607432). (300215) (Updated 05-Apr-2021)

UniProtKB/Swiss-Prot : 72 Lissencephaly, X-linked 2: A classic type lissencephaly associated with abnormal genitalia. Patients have severe congenital or postnatal microcephaly, lissencephaly, agenesis of the corpus callosum, neonatal-onset intractable epilepsy, poor temperature regulation, chronic diarrhea, and ambiguous or underdeveloped genitalia.

Related Diseases for Lissencephaly, X-Linked, 2

Diseases in the Lissencephaly, X-Linked, 1 family:

Lissencephaly, X-Linked, 2

Diseases related to Lissencephaly, X-Linked, 2 via text searches within MalaCards or GeneCards Suite gene sharing:

(show all 31)
# Related Disease Score Top Affiliating Genes
1 mental retardation, x-linked, with or without seizures, arx-related 31.0 LOC109610631 ARX
2 partington x-linked mental retardation syndrome 30.9 LOC109610631 ARX
3 developmental and epileptic encephalopathy 1 30.9 LOC109610631 ARX
4 non-syndromic x-linked intellectual disability 29.8 LOC109610631 ARX
5 west syndrome 29.7 LOC109610631 ARX
6 chromosome xq26.3 duplication syndrome 11.3
7 lissencephaly 11.0
8 corpus callosum, agenesis of, with abnormal genitalia 10.9
9 cryptorchidism, unilateral or bilateral 10.3
10 lissencephaly, x-linked, 1 10.3
11 penis agenesis 10.3
12 exocrine pancreatic insufficiency 10.2
13 dcx-related disorders 10.2
14 myoclonus 10.2
15 neuronal migration disorders 10.2
16 microcephaly 10.0
17 pachygyria 10.0
18 hypotonia 10.0
19 vesicoureteral reflux 1 9.9
20 miller-dieker lissencephaly syndrome 9.9
21 gonadal agenesis 9.9
22 patent ductus arteriosus 1 9.9
23 alacrima, achalasia, and mental retardation syndrome 9.9
24 corpus callosum, agenesis of, with facial anomalies and cerebellar ataxia 9.9
25 disease by infectious agent 9.9
26 diarrhea 9.9
27 hypogonadism 9.9
28 febrile seizures 9.9
29 basal encephalocele 9.7 LOC109610631 ARX
30 lissencephaly 2 9.7 LOC109610631 ARX
31 early infantile epileptic encephalopathy 9.5 LOC109610631 ARX

Graphical network of the top 20 diseases related to Lissencephaly, X-Linked, 2:

Diseases related to Lissencephaly, X-Linked, 2

Symptoms & Phenotypes for Lissencephaly, X-Linked, 2

Human phenotypes related to Lissencephaly, X-Linked, 2:

58 31 (show all 43)
# Description HPO Frequency Orphanet Frequency HPO Source Accession
1 intellectual disability 58 31 hallmark (90%) Very frequent (99-80%) HP:0001249
2 agenesis of corpus callosum 58 31 hallmark (90%) Very frequent (99-80%) HP:0001274
3 global developmental delay 58 31 hallmark (90%) Very frequent (99-80%) HP:0001263
4 microcephaly 58 31 hallmark (90%) Very frequent (99-80%) HP:0000252
5 cryptorchidism 58 31 hallmark (90%) Very frequent (99-80%) HP:0000028
6 hypoplasia of penis 58 31 hallmark (90%) Very frequent (99-80%) HP:0008736
7 ambiguous genitalia 58 31 hallmark (90%) Very frequent (99-80%) HP:0000062
8 pachygyria 58 31 hallmark (90%) Very frequent (99-80%) HP:0001302
9 seizure 31 hallmark (90%) HP:0001250
10 malabsorption 58 31 frequent (33%) Frequent (79-30%) HP:0002024
11 hypohidrosis 58 31 frequent (33%) Frequent (79-30%) HP:0000966
12 ventriculomegaly 58 31 frequent (33%) Frequent (79-30%) HP:0002119
13 hypotonia 31 frequent (33%) HP:0001252
14 spasticity 58 31 occasional (7.5%) Occasional (29-5%) HP:0001257
15 prominent forehead 58 31 occasional (7.5%) Occasional (29-5%) HP:0011220
16 micrognathia 58 31 occasional (7.5%) Occasional (29-5%) HP:0000347
17 exocrine pancreatic insufficiency 58 31 occasional (7.5%) Occasional (29-5%) HP:0001738
18 aganglionic megacolon 58 31 occasional (7.5%) Occasional (29-5%) HP:0002251
19 patent ductus arteriosus 58 31 occasional (7.5%) Occasional (29-5%) HP:0001643
20 ventricular septal defect 58 31 occasional (7.5%) Occasional (29-5%) HP:0001629
21 seizures 58 Very frequent (99-80%)
22 hyperreflexia 31 HP:0001347
23 high palate 31 HP:0000218
24 muscular hypotonia 58 Frequent (79-30%)
25 wide nasal bridge 31 HP:0000431
26 feeding difficulties in infancy 31 HP:0008872
27 low-set ears 31 HP:0000369
28 specific learning disability 31 HP:0001328
29 micropenis 31 HP:0000054
30 thin upper lip vermilion 31 HP:0000219
31 long philtrum 31 HP:0000343
32 death in infancy 58 Frequent (79-30%)
33 prominent nasal bridge 31 HP:0000426
34 high forehead 31 HP:0000348
35 severe global developmental delay 31 HP:0011344
36 decreased testicular size 31 HP:0008734
37 wide anterior fontanel 31 HP:0000260
38 profound global developmental delay 31 HP:0012736
39 diarrhea 31 HP:0002014
40 generalized hypotonia 31 HP:0001290
41 duane anomaly 31 HP:0009921
42 long upper lip 31 HP:0011341
43 gliosis 31 HP:0002171

Symptoms via clinical synopsis from OMIM®:

57 (Updated 05-Apr-2021)
Neurologic Central Nervous System:
enlarged ventricles
agenesis of the corpus callosum
psychomotor retardation, profound
Head And Neck Face:
long philtrum

Head And Neck Head:
high forehead
large anterior fontanelle

Head And Neck Mouth:
long upper lip
thin upper lip
high-arched palate

Endocrine Features:
hypothalamic dysfunction
impaired temperature regulation

Head And Neck Nose:
wide nasal bridge
prominent nasal root
pinched nasal alae

Head And Neck Ears:
low-set ears

Genitourinary External Genitalia Male:
ambiguous genitalia
small penis
small testes
underdeveloped scrotal folds

Abdomen Gastrointestinal:
poor feeding
diarrhea, chronic

Head And Neck Eyes:
thin optic nerves
duane anomaly (reported in 1 female)

Clinical features from OMIM®:

300215 (Updated 05-Apr-2021)

UMLS symptoms related to Lissencephaly, X-Linked, 2:

snoring; thick skin

Drugs & Therapeutics for Lissencephaly, X-Linked, 2

Search Clinical Trials , NIH Clinical Center for Lissencephaly, X-Linked, 2

Genetic Tests for Lissencephaly, X-Linked, 2

Genetic tests related to Lissencephaly, X-Linked, 2:

# Genetic test Affiliating Genes
1 Lissencephaly 2, X-Linked 29 ARX
2 Hydranencephaly with Abnormal Genitalia 29

Anatomical Context for Lissencephaly, X-Linked, 2

MalaCards organs/tissues related to Lissencephaly, X-Linked, 2:

Brain, Testes, Cortex, Thalamus

Publications for Lissencephaly, X-Linked, 2

Articles related to Lissencephaly, X-Linked, 2:

# Title Authors PMID Year
Mutations of ARX are associated with striking pleiotropy and consistent genotype-phenotype correlation. 57 61 6
14722918 2004
Mutation of ARX causes abnormal development of forebrain and testes in mice and X-linked lissencephaly with abnormal genitalia in humans. 6 57
12379852 2002
X-linked lissencephaly with absent corpus callosum and ambiguous genitalia (XLAG): clinical, magnetic resonance imaging, and neuropathological findings. 6 57
11891829 2002
Distinct DNA binding and transcriptional repression characteristics related to different ARX mutations. 6
22252899 2012
Targeted loss of Arx results in a developmental epilepsy mouse model and recapitulates the human phenotype in heterozygous females. 57
19439424 2009
Expansion of the ARX spectrum. 57
18462864 2008
ARX mutations in X-linked lissencephaly with abnormal genitalia. 6
12874405 2003
X-linked lissencephaly with ambiguous genitalia: delineation of further case. 57
10982975 2000
X-linked lissencephaly with absent corpus callosum and ambiguous genitalia. 57
10494089 1999
New X-linked syndrome with seizures, acquired micrencephaly, and agenesis of the corpus callosum. 57
1605226 1992

Variations for Lissencephaly, X-Linked, 2

ClinVar genetic disease variations for Lissencephaly, X-Linked, 2:

6 (show all 37)
# Gene Name Type Significance ClinVarId dbSNP ID Position
1 ARX NM_139058.3(ARX):c.1105G>T (p.Glu369Ter) SNV Pathogenic 11201 rs104894746 GRCh37: X:25028391-25028391
GRCh38: X:25010274-25010274
2 ARX ARX, 32-BP DEL, NT420 Deletion Pathogenic 11190 GRCh37:
3 ARX NM_139058.3(ARX):c.1117C>T (p.Gln373Ter) SNV Pathogenic 11193 rs104894740 GRCh37: X:25028379-25028379
GRCh38: X:25010262-25010262
4 ARX ARX, EX1-2DEL Deletion Pathogenic 11195 GRCh37:
5 ARX NM_139058.3(ARX):c.1028T>A (p.Leu343Gln) SNV Pathogenic 11197 rs104894741 GRCh37: X:25031084-25031084
GRCh38: X:25012967-25012967
6 ARX NM_139058.3(ARX):c.232G>T (p.Glu78Ter) SNV Pathogenic 11205 rs267606666 GRCh37: X:25031880-25031880
GRCh38: X:25013763-25013763
7 ARX NM_139058.3(ARX):c.525C>G (p.Tyr175Ter) SNV Pathogenic 689380 rs1601948603 GRCh37: X:25031587-25031587
GRCh38: X:25013470-25013470
8 ARX NM_139058.3(ARX):c.790del (p.Arg264fs) Deletion Pathogenic 287023 rs886043552 GRCh37: X:25031322-25031322
GRCh38: X:25013205-25013205
9 ARX NM_139058.3(ARX):c.995G>A (p.Arg332His) SNV Pathogenic 11192 rs111033612 GRCh37: X:25031117-25031117
GRCh38: X:25013000-25013000
10 ARX NM_139058.3(ARX):c.1372del (p.Ala458fs) Deletion Pathogenic 157744 rs587783187 GRCh37: X:25025304-25025304
GRCh38: X:25007187-25007187
11 ARX NM_139058.3(ARX):c.1414C>T (p.Arg472Ter) SNV Pathogenic 157746 rs587783189 GRCh37: X:25025262-25025262
GRCh38: X:25007145-25007145
12 LOC109610631 , ARX NM_139058.3(ARX):c.335_368del (p.Ala112fs) Deletion Pathogenic 157756 rs587783199 GRCh37: X:25031744-25031777
GRCh38: X:25013627-25013660
13 ARX NM_139058.3(ARX):c.617del (p.Gly206fs) Deletion Pathogenic 157759 rs587783202 GRCh37: X:25031495-25031495
GRCh38: X:25013378-25013378
14 ARX NM_139058.3(ARX):c.995G>T (p.Arg332Leu) SNV Pathogenic 157765 rs111033612 GRCh37: X:25031117-25031117
GRCh38: X:25013000-25013000
15 ARX NM_139058.3(ARX):c.562_563delinsTA (p.Ala188Ter) Indel Pathogenic 210335 rs797045303 GRCh37: X:25031549-25031550
GRCh38: X:25013432-25013433
16 ARX NM_139058.3(ARX):c.1096del (p.Asp366fs) Deletion Pathogenic 210316 rs797045289 GRCh37: X:25028400-25028400
GRCh38: X:25010283-25010283
17 LOC109610631 , ARX NM_139058.3(ARX):c.409dup (p.Glu137fs) Duplication Pathogenic 210330 rs797045298 GRCh37: X:25031702-25031703
GRCh38: X:25013585-25013586
18 ARX NM_139058.3(ARX):c.1337dup (p.Pro447fs) Duplication Pathogenic 210319 rs797045291 GRCh37: X:25025338-25025339
GRCh38: X:25007221-25007222
19 LOC109610631 , ARX NM_139058.2(ARX):c.304_305ins21 (p.?) Insertion Pathogenic 210326 GRCh37: X:25031807-25031808
GRCh38: X:25013690-25013691
20 ARX NM_139058.3(ARX):c.1449-82_1469dup Duplication Pathogenic 210320 rs1556046904 GRCh37: X:25023006-25023007
GRCh38: X:25004889-25004890
21 ARX NM_139058.3(ARX):c.1164_1165insCAAAG (p.Ala389fs) Insertion Pathogenic 210318 rs797045290 GRCh37: X:25025511-25025512
GRCh38: X:25007394-25007395
22 ARX NM_139058.3(ARX):c.1471dup (p.Leu491fs) Duplication Pathogenic 210321 rs797045292 GRCh37: X:25023004-25023005
GRCh38: X:25004887-25004888
23 ARX NM_139058.3(ARX):c.1141del (p.Ala381fs) Deletion Pathogenic 434396 rs1556049694 GRCh37: X:25025535-25025535
GRCh38: X:25007418-25007418
24 ARX NM_139058.3(ARX):c.1535_1549delinsGGCGCAG (p.Val512fs) Indel Pathogenic 434399 rs1556046720 GRCh37: X:25022927-25022941
GRCh38: X:25004810-25004824
25 ARX NM_139058.3(ARX):c.1465del (p.Ala489fs) Deletion Pathogenic 157748 rs587783191 GRCh37: X:25023011-25023011
GRCh38: X:25004894-25004894
26 LOC109610631 , ARX NM_139058.3(ARX):c.306_308GGC[18] (p.Ala108_Ala115dup) Microsatellite Pathogenic 210327 rs387906492 GRCh37: X:25031776-25031777
GRCh38: X:25013659-25013660
27 ARX NM_139058.3(ARX):c.1223_1226dup (p.Leu410fs) Microsatellite Pathogenic 995570 GRCh37: X:25025449-25025450
GRCh38: X:25007332-25007333
28 ARX NM_139058.3(ARX):c.1187dup (p.Gly397fs) Duplication Pathogenic 11194 rs1328291159 GRCh37: X:25025488-25025489
GRCh38: X:25007371-25007372
29 LOC109610631 , ARX NM_139058.3(ARX):c.441_464dup (p.Ala148_Ala155dup) Duplication Pathogenic 96455 rs398124510 GRCh37: X:25031647-25031648
GRCh38: X:25013530-25013531
30 LOC109610631 , ARX NM_139058.3(ARX):c.306_308GGC[17] (p.Ala109_Ala115dup) Microsatellite Pathogenic 11186 rs387906492 GRCh37: X:25031776-25031777
GRCh38: X:25013659-25013660
31 ARX NM_139058.3(ARX):c.1120-82_1469dup Duplication Pathogenic 210317 GRCh37: X:25023006-25023007
GRCh38: X:25004889-25004890
32 LOC109610631 , ARX NM_139058.3(ARX):c.426_461dup (p.Gly143_Ala154dup) Duplication Likely pathogenic 210331 rs1556056131 GRCh37: X:25031650-25031651
GRCh38: X:25013533-25013534
33 ARX NM_139058.3(ARX):c.1121T>A (p.Val374Asp) SNV Likely pathogenic 157740 rs587783183 GRCh37: X:25025555-25025555
GRCh38: X:25007438-25007438
34 ARX NM_139058.3(ARX):c.1134C>A (p.Asn378Lys) SNV Likely pathogenic 157741 rs587783184 GRCh37: X:25025542-25025542
GRCh38: X:25007425-25007425
35 LOC109610631 , ARX NM_139058.3(ARX):c.379C>T (p.Pro127Ser) SNV Uncertain significance 1031153 GRCh37: X:25031733-25031733
GRCh38: X:25013616-25013616
36 ARX NM_139058.3(ARX):c.1170C>T (p.Gly390=) SNV Uncertain significance 234531 rs761632870 GRCh37: X:25025506-25025506
GRCh38: X:25007389-25007389
37 ARX NM_139058.3(ARX):c.187G>A (p.Ala63Thr) SNV Uncertain significance 581240 rs769996976 GRCh37: X:25033668-25033668
GRCh38: X:25015551-25015551

UniProtKB/Swiss-Prot genetic disease variations for Lissencephaly, X-Linked, 2:

# Symbol AA change Variation ID SNP ID
1 ARX p.Arg332His VAR_015178 rs111033612
2 ARX p.Leu343Gln VAR_015179 rs104894741
3 ARX p.Arg332Pro VAR_033260
4 ARX p.Pro353Arg VAR_033262
5 ARX p.Ala521Thr VAR_033263 rs746120093

Expression for Lissencephaly, X-Linked, 2

Search GEO for disease gene expression data for Lissencephaly, X-Linked, 2.

Pathways for Lissencephaly, X-Linked, 2

GO Terms for Lissencephaly, X-Linked, 2

Sources for Lissencephaly, X-Linked, 2

9 Cosmic
10 dbSNP
11 DGIdb
17 EFO
18 ExPASy
19 FMA
28 GO
29 GTR
31 HPO
32 ICD10
33 ICD10 via Orphanet
37 LifeMap
41 MedGen
44 MeSH
45 MESH via Orphanet
46 MGI
49 NCI
50 NCIt
54 Novoseek
56 OMIM via Orphanet
57 OMIM® (Updated 05-Apr-2021)
61 PubMed
69 Tocris
71 UMLS via Orphanet
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