Genes associated with “abnormal brain morphology”

322 genes foundHPO: Abnormal brain morphologyOpen Targets: Abnormal brain morphology5 PanelApp panels
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

18 genes
1
PDGFRB →

platelet derived growth factor receptor beta

27
score
Panel: Red ↑P2G #10GTR ↑
Frequency
-
P/LP Variants
-
OT Score
0.79
2
SLC25A19 →

solute carrier family 25 member 19

26
score
ClinGen: LimitedP2G #46GTR ↑

Primary microcephaly

Frequency
100%
n=11
P/LP Variants
-
OT Score
0.79
3
TUBA1A →

tubulin alpha 1a

25
score
ClinGen: DefinitiveGTR ↑
Frequency
-
P/LP Variants
1
OT Score
0.66
4
24
score
ClinGen: DefinitivePanel: Green ↑P2G #2GTR ↑

Hydrocephalus

Frequency
75%
n=4
P/LP Variants
-
OT Score
-
5
PDGFB →

platelet derived growth factor subunit B

23
score
P2G #28GTR ↑

Cerebellar calcifications

Frequency
35%
n=31
P/LP Variants
-
OT Score
0.78
6
PLA2G6 →

phospholipase A2 group VI

23
score
ClinGen: DefinitiveGTR ↑
Frequency
-
P/LP Variants
2
OT Score
0.64
7
STIL →

STIL centriolar assembly protein

22
score
ClinGen: DefinitiveGTR ↑
Frequency
-
P/LP Variants
2
OT Score
0.79
8
22
score
ClinGen: DefinitivePanel: Green ↑P2G #1GTR ↑

Chiari malformation

Frequency
-
P/LP Variants
-
OT Score
-
9
COL4A1 →

collagen type IV alpha 1 chain

22
score
ClinGen: DefinitiveP2G #14GTR ↑
Frequency
-
P/LP Variants
-
OT Score
0.68
21KIF11
Def

kinesin family member 11

21PCNT
DefP:G

pericentrin

21DYRK1A
Def

dual specificity tyrosine phosphorylation regulated kinase 1A

21CEP152
Def

centrosomal protein 152

20MCPH1
Def

microcephalin 1

20EML1
Def

Subcortical band heterotopia

20SLC18A2
Def
20TBCD
Def

Secondary microcephaly

20TUBB2B
Def

Microcephaly

Consider

84 genes
19RNU4ATAC
DefP:G

RNA, U4atac small nuclear

18ERCC6
DefP:G

Microcephaly

18KNL1

Cerebellar vermis hypoplasia

17SLC20A2

solute carrier family 20 member 2

16KAT6B
Def

Thin corpus callosum

16WDR62
Def

Pachygyria

16LMNB1
Def

lamin B1

15RAB18
ModP:G

Ventriculomegaly

15GRIP1
DefP:G
15NDE1
Def

nudE neurodevelopment protein 1

15PNKP
Def

polynucleotide kinase 3'-phosphatase

15CDK5RAP2
Def

CDK5 regulatory subunit associated protein 2

15NIPBL
DefP:G
15TUBGCP6
Def

tubulin gamma complex component 6

15ASPM
Def

assembly factor for spindle microtubules

15CEP135

Primary microcephaly

14DCX
Def

doublecortin

14L1CAM
Def

L1 cell adhesion molecule

14PTCH1
Def

Holoprosencephaly

14INPP5E
Def

Molar tooth sign on MRI

13ACTB
Def

Agenesis of corpus callosum

13ERCC8
DefP:G

Ventriculomegaly

13ITPR1
Def
13ACE
Def

angiotensin I converting enzyme

13DHCR7
DefP:G
13IDDABS

INTELLECTUAL DEVELOPMENTAL DISORDER WITH ABNORMAL BEHAVIOR, MICROCEPHALY, AND SHORT STATURE; IDDABS

13MCIDDS

MICROCEPHALY, CATARACTS, IMPAIRED INTELLECTUAL DEVELOPMENT, AND DYSTONIA WITH ABNORMAL STRIATUM; MCIDDS

13NEDAMSS

NEURODEVELOPMENTAL DISORDER WITH REGRESSION, ABNORMAL MOVEMENTS, LOSS OF SPEECH, AND SEIZURES; NEDAMSS

13SEMDAD

SPONDYLOEPIMETAPHYSEAL DYSPLASIA WITH ABNORMAL DENTITION; SEMDAD

13SOX3
ModP:G
13THMA1

THYROID HORMONE METABOLISM, ABNORMAL, 1; THMA1

13KIF14

Simplified gyral pattern

13ZNF335

Simplified gyral pattern

13PAK3
Def

p21 (RAC1) activated kinase 3

12TCF4
Def

Hypoplasia of the corpus callosum

12ATP1A3
DefP:G

Microcephaly

12HMGCR
Mod

3-hydroxy-3-methylglutaryl-CoA reductase

12TCOF1
DefP:G

Hydrocephalus

12ANKLE2

ankyrin repeat and LEM domain containing 2

12FANCB
DefP:G

Cerebellar hypoplasia

12TUBGCP4

tubulin gamma complex component 4

12MACF1
Mod

microtubule actin crosslinking factor 1

11LMNB2

lamin B2

11MFSD2A

MFSD2 lysolipid transporter A, lysophospholipid

11EYA1
DefP:G

Abnormal cerebral morphology

11SPTAN1
Def

Microcephaly

11GFAP
Def

Abnormal dentate nucleus morphology

11RAB3GAP2
DefP:G

Microcephaly

10PDE3A

phosphodiesterase 3A

10NCAPD3

non-SMC condensin II complex subunit D3

10SASS6

SAS-6 centriolar assembly protein

10NOTCH3
Lim
10TSEN54

Progressive microcephaly

10ALDH18A1
DefP:G

Cerebral cortical atrophy

10NCAPD2

non-SMC condensin I complex subunit D2

10WDR11

WD repeat domain 11

9SSTR4

somatostatin receptor 4

9ARF3

ARF GTPase 3

9PTGS2

prostaglandin-endoperoxide synthase 2

9PHC1

polyhomeotic homolog 1

9AP4B1
Def
9GALC
Def
9MTO1
Def
9SNX14
Def
9SYNE1
Def
9VARS1
Def
9VPS13B
Def
9PRUNE1
9ASXL1
Def
9ASXL3
Def
9BCOR
Def
9PTCHD1
Def
9RAB3GAP1
DefP:G

Cerebral atrophy

9SETD2
Def

Hypoplasia of the pons

9GPSM2
Def

Ventriculomegaly

9TSC1
DefSF

Hemimegalencephaly

8POLE
DefSF

Microcephaly

8ZNF423
Mod
8RXYLT1
Def

Type II lissencephaly

8TRIO
Def

Microcephaly

8GLDC
Def

Agenesis of corpus callosum

8IGF1R
P:G

Hypoplasia of the corpus callosum

8RBM8A
Def

Cavum septum pellucidum

8ZEB2
Def

Hypoplasia of the corpus callosum

Possible

162 genes — click to expand
8ARID1A
Def

Abnormal corpus callosum morphology

7CRPPA
Def

Hydrocephalus

7ALDH7A1
Def
7CLN6
Def
7HADH
Def
7IQSEC2
Def
7MTRFR
Def
7NGLY1
Def
7OPA1
Def
7PGM3
Def
7PIGN
Def
7PLCB1
Def
7POMT2
Def
7RARS2
Def
7SPG11
Def
7SUMF1
Def
7SYNCRIP
Def
7TRNT1
Def
7WDFY3
Def

?Microcephaly 18, primary, autosomal dominant

7PNPT1
Mod

Cerebellar atrophy

7MAPK1

Microcephaly

7DDX3X
Def

Microcephaly

6SIN3A
Def

Ventriculomegaly

6LINS1
Def

Microcephaly

6CACNA1H
6CDK10
6DHX37
6PTPRT
6RAC3
6ANK3
Mod
6CRBN
Mod
6BCAP31
Def

Cerebral atrophy

6NFIX
Def

Hypoplasia of the corpus callosum

6SYNGAP1
Def

Microcephaly

6CWF19L1
Def

Cerebellar hypoplasia

6AUH
Def

Abnormal cerebral white matter morphology

6KISS1R

Elevated circulating follicle stimulating hormone level

6SLC39A8
Lim

Cerebellar vermis atrophy

5C2CD3
Def

Partial agenesis of the corpus callosum

5DAG1
Def

Polymicrogyria

5FKRP
Def

Dandy-Walker malformation

5FKTN
Def

Dandy-Walker malformation

5KCNT1
Def

Microcephaly

5POMGNT1
Def

Hydrocephalus

5STT3A
Def

Microcephaly

5CSNK2A1
Def

Microcephaly

5POLR2A
Def

Ventriculomegaly

5ARID1B
Def

Microcephaly

5CABAC

CEREBELLAR ATAXIA, BRAIN ABNORMALITIES, AND CARDIAC CONDUCTION DEFECTS; CABAC

5CPLX1

Ventriculomegaly

5EPB41L1
Lim
5EXOSC5

Cerebellar ataxia, brain abnormalities, and cardiac conduction defects

5HRM2

Hair, curly

5NSD2
Def

Microcephaly

5SMARCA1
Lim
5DCC
Def

Fusion of the left and right thalami

5FAR1
Mod

Microcephaly

5BRCA2
DefSF

Microcephaly

5KIF1A
Def

Microcephaly

5AMPD2

Cerebellar hypoplasia

5CEP55

Cerebellar hypoplasia

5GORAB
Def

Microcephaly

5ASNS
Def

Global brain atrophy

5NFU1
Def

Corpus callosum atrophy

5PIGS
Def

Cerebral cortical atrophy

5SCO2
Def

Diffuse white matter abnormalities

5EARS2
Def

Agenesis of corpus callosum

5ARHGEF15

Deep cerebral white matter hyperintensities

4COG5
Def

Cerebellar atrophy

4DEPDC5
Def

Focal cortical dysplasia type I

4TWNK
Def

Cerebellar cortical atrophy

4B4GALNT1
Def

Cerebral cortical atrophy

4AGBL2
4ARHGAP21
4ARL8B
4ASTN1
4BHLHE40
4CDH4
4CEP162
4CHCHD4
4CHL1
4CNTN4
Dis
4CNTN6
Dis
4CYB5R4
4DARS1
4DOP1A
4DSCAML1
4EDEM1
4FAM222A
4GTF3C1
4HTR1E
4IGFBP4
4IL5RA
4ITGA7
4KANK1
4KLHL15
4LARP7
4LRRN1
4ME1
4MRAP2
4MXRA8
4NT5E
4OGDHL
4PLEKHG2
4PRSS35
4PWWP2A
4RIPPLY2
4RIPPLY2-CYB5R4
4ROS1
4RWDD2A
4SETMAR
4SLITRK5
4SNAP91
4SNAPIN
4SNHG5
4TBX18
4TTC1
4TTI1
4TUT1
4UBE3D
4UBQLN1
4ULK2
4USP11
4WNT7A
4NDUFS1
Def

Focal T2 hyperintense basal ganglia lesion

4PIGO
Def

Microcephaly

4ALG2
Str

Microcephaly

4HID1

Anterior pituitary hypoplasia

4AP2M1
Def

Abnormal cerebral white matter morphology

4CNTNAP2
Def

Focal cortical dysplasia

4GNAO1
Def

Cerebellar atrophy

4NADK2
Mod

Hypoplasia of the corpus callosum

4MYORG

Basal ganglia calcification

4ACSL4
Def

Microcephaly

4TRPM3
Def

Ventriculomegaly

4NDUFA11
Lim

Secondary microcephaly

3CPLANE1
Def

Porencephalic cyst

3PIDD1
Def

Microcephaly

3RAB11B

Cerebellar vermis hypoplasia

3ABAT
Mod

Cerebellar hypoplasia

3GDAP2
Str

Cerebral cortical atrophy

3DDX59

Microcephaly

3ACTG1
Def

Pachygyria

3ARFGEF2
Def

Hypoplasia of the corpus callosum

3BRAT1
Def

Progressive microcephaly

3D2HGDH
Def

Subependymal cysts

3DPM1
Def

Secondary microcephaly

3EPHB4
Def

Vein of Galen aneurysmal malformation

3ERCC4
Def

Brain atrophy

3HEPACAM
Def

Diffuse spongiform leukoencephalopathy

3LARGE1
Def

Hypoplasia of the pons

3LRP5
Def

Microcephaly

3LYRM7
Def

Atrophy/Degeneration affecting the brainstem

3NAXE
Def

Brain atrophy

3POLR3A
Def

Hydrocephalus

3POMT1
Def

Pachygyria

3PPT1
Def

Progressive microcephaly

3PRKDC
Def

Microcephaly

3ST3GAL5
Def

Microcephaly

3TACO1
Def

Leukoencephalopathy

3VPS33B
Def

Microcephaly

3WAC
Def

Hypoplasia of the corpus callosum

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.