Genes associated with “intellectual disability

636 genes foundHPO: Intellectual disabilityOpen Targets: Intellectual disability1 PanelApp panel
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:
HPOClinVarPhen2GeneOpen TargetsPanelApp
hover for details

Strong Candidates

104 genes
1
AHDC1

AT-hook DNA binding motif containing 1

56
score
ClinGen: DefinitivePanel: GreenGTR ↑

Moderate intellectual disability

Frequency
62%
n=13
P/LP Variants
2
OT Score
0.71
2
MED13L

mediator complex subunit 13L

54
score
ClinGen: DefinitivePanel: GreenGTR ↑
Frequency
-
P/LP Variants
5
OT Score
0.67
3
CTCF

CCCTC-binding factor

52
score
ClinGen: DefinitivePanel: GreenGTR ↑
Frequency
-
P/LP Variants
3
OT Score
0.66
4
POGZ

pogo transposable element derived with ZNF domain

52
score
ClinGen: DefinitivePanel: GreenGTR ↑
Frequency
-
P/LP Variants
3
OT Score
0.63
50
score
ClinGen: DefinitivePanel: GreenGTR ↑

Intellectual disability

Frequency
100%
n=25
P/LP Variants
3
OT Score
-
6
DDX3X

DEAD-box helicase 3 X-linked

47
score
ClinGen: DefinitivePanel: GreenGTR ↑
Frequency
-
P/LP Variants
1
OT Score
0.63
7
SLC6A8

solute carrier family 6 member 8

45
score
ClinGen: DefinitivePanel: GreenGTR ↑

Intellectual disability

Frequency
100%
n=3
P/LP Variants
4
OT Score
0.62
42
score
ClinGen: DefinitivePanel: GreenGTR ↑

Intellectual disability

Frequency
100%
n=9
P/LP Variants
3
OT Score
-
9
MECP2

methyl-CpG binding protein 2

41
score
ClinGen: DefinitivePanel: GreenGTR ↑

Intellectual disability

Frequency
100%
n=5
P/LP Variants
5
OT Score
0.56
41MYT1L
DefP:G

myelin transcription factor 1 like

40CASK
DefP:G

Moderate intellectual disability

39FOXP1
DefP:G
39KAT6A
DefP:G
39SLC2A1
DefP:G

solute carrier family 2 member 1

38KDM5C
DefP:G
38KIF11
DefP:G
38NAA15
DefP:G
38KMT2C
DefP:G

lysine methyltransferase 2C

35ADNP
DefP:G
34MTOR
DefP:G

mechanistic target of rapamycin kinase

34ZMYND11
DefP:G

Mild intellectual disability

34BCAP31
DefP:G

Severe intellectual disability

33KAT6B
DefP:G
33KMT2A
DefP:G

Intellectual disability

33ASH1L
DefP:G

ASH1 like histone lysine methyltransferase

33AFF2
DefP:G
33ASXL3
DefP:G
33BRWD3
DefP:G
33GATAD2B
DefP:G
33IL1RAPL1
DefP:G
33TBL1XR1
DefP:G

Intellectual disability

33KANSL1
DefP:G

KAT8 regulatory NSL complex subunit 1

32BCL11A
DefP:G

BCL11 transcription factor A

32MED12
DefP:G
32TCF20
DefP:G

transcription factor 20

32RAC1
DefP:G

Intellectual disability

31ATRX
DefP:G

Severe intellectual disability

31ITPR1
DefP:G

Intellectual disability

31EP300
DefP:G#14
31ANKRD11
DefP:G

Intellectual disability

30ATP8A2
DefP:G
30PIDD1
DefP:G

p53-induced death domain protein 1

30CREBBP
DefP:G
30GMPPA
DefP:G

Intellectual disability

29SATB2
DefP:G

SATB homeobox 2

29STXBP1
DefP:G

syntaxin binding protein 1

29KMT2E
DefP:G

lysine methyltransferase 2E (inactive)

28KDM6A
DefP:G

Mild intellectual disability

28KMT2D
DefP:G

Mild intellectual disability

28DLG3
DefP:G

Intellectual disability

28RPS6KA3
DefP:G#17
28TUSC3
DefP:G
28SHANK3
DefP:G
28CHD7
DefP:G#2
27JARID2
DefP:G
27KIF1A
DefP:G
27WDR62
DefP:G

Intellectual disability

27SETD5
DefP:G
27SIN3A
DefP:G
27CHD5
P:G

chromodomain helicase DNA binding protein 5

26DYRK1A
DefP:G
26CAMK2B
P:G

calcium/calmodulin dependent protein kinase II beta

26QRICH1
DefP:G

glutamine rich 1

25ARID1A
DefP:G
25CHD4
DefP:G
25CNNM2
DefP:G
25CTNNB1
DefP:G
25NSUN2
DefP:G
25USP9X
DefP:G
25TCF4
DefP:G
25UBE3A
DefP:G
25KCNN2
P:G

potassium calcium-activated channel subfamily N member 2

24IKBKG
DefP:G#19
24MED23
ModP:G

Profound intellectual disability

24EZH2
DefP:G
24PTPN11
DefP:G

Intellectual disability

24NFIX
DefP:G
23ANKRD17
DefP:G
23CNKSR2
DefP:G
23GRIN2B
DefP:G
23MEF2C
DefP:G
23HPRT1
DefP:G
23CEP290
DefP:G

Intellectual disability

23PAH
DefP:G
23PTEN
DefSFP:G#4

Mild intellectual disability

23OCRL
DefP:G
22RAI1
DefP:G

Intellectual disability

22FGFR3
DefP:R#1
22GLI3
DefP:A
21KMT2B
DefP:G

Intellectual disability

21KCNQ2
DefP:G

Intellectual disability

21SETD2
DefP:G

Intellectual disability

21ARID1B
DefP:G
21CNOT1
DefP:G
21EFTUD2
DefP:G
21PHIP
DefP:G
21SYNGAP1
DefP:G
21SMARCA4
DefP:G
20SCN8A
DefP:G

Borderline intellectual disability

20LINS1
DefP:G

Intellectual disability

20CBS
DefP:G

Intellectual disability

20CAMTA1
DefP:G
20CHD8
DefP:G
20NUS1
DefP:G

Consider

243 genes
20PPP2R1A
DefP:G
20SOS1
DefP:G
20PURA
DefP:G

purine rich element binding protein A

20NSDHL
ModP:G#13

Intellectual disability

19NBEA
DefP:G

neurobeachin

19PACS1
DefP:G

Intellectual disability

19ARID2
DefP:G
19ASXL1
DefP:G
19CACNA1C
DefP:G
19KDM5B
ModP:G
19LAMP2
DefP:G
19SOX3
ModP:A

Mild intellectual disability

19TLK2
DefP:G
19ZEB2
DefP:G
19CAMK2A
DefP:G

calcium/calmodulin dependent protein kinase II alpha

19GABRB2
DefP:G

gamma-aminobutyric acid type A receptor subunit beta2

19NDE1
DefP:G

Severe intellectual disability

19PPP2R5D
DefP:G

protein phosphatase 2 regulatory subunit B'delta

19ARFGEF1
DefP:G

ARF guanine nucleotide exchange factor 1

18AGA
DefP:G
18DEPDC5
DefP:G
18GRIN1
DefP:G
18LAMA1
P:G
18TUBA1A
DefP:G

tubulin alpha 1a

18YY1
DefP:G

YY1 transcription factor

18SYP
ModP:G

Intellectual disability

18POU3F3
DefP:G

POU class 3 homeobox 3

17PCGF2
DefP:G

polycomb group ring finger 2

17KCNH1
DefP:G

potassium voltage-gated channel subfamily H member 1

17SMARCC2
DefP:G

SWI/SNF related BAF chromatin remodeling complex subunit C2

17EBF3
DefP:G
17FOXG1
DefP:G
17FRMPD4
DefP:G

FERM and PDZ domain containing 4

17L1CAM
DefP:G
17NR2F1
DefP:G
17OTC
DefSFP:G
17SLC9A6
DefP:G
17SON
DefP:G
17TRIP12
DefP:G
17FLNA
DefP:R

Intellectual disability

17TSPAN7
ModP:A

Intellectual disability

17SHOC2
DefP:G

Intellectual disability

17MAP2K1
DefP:G

Intellectual disability

17ERCC2
DefP:G

Intellectual disability

17HNF1B
DefP:A
17HNRNPU
DefP:G
17KIDINS220
DefP:G
17MBD5
DefP:G
17SPG11
DefP:G
17GNB2
P:G

Intellectual disability

17SLC17A5
DefP:G

Intellectual disability

17SURF1
DefP:G

Intellectual disability

16EEF1A2
DefP:G

Severe intellectual disability

16AP4M1
DefP:G

Intellectual disability

16ACTB
DefP:G
16GRIA3
DefP:G
16GRIK2
DefP:G
16PIGV
ModP:G
16SRCAP
DefP:G

Intellectual disability

16PIK3R2
DefP:G

Profound intellectual disability

16PDHX
DefP:G

Intellectual disability

16USP27X
LimP:A

Intellectual disability

15ARF3
P:G

ARF GTPase 3

15KDM5A
LimP:G

lysine demethylase 5A

15COL4A1
DefP:G
15EHMT1
DefP:G
15IQSEC2
DefP:G
15IRF2BPL
DefP:G
15KMT5B
DefP:G
15LZTR1
DefSFP:G
15MMAA
DefP:G
15MTHFR
DefP:G
15NTRK1
DefP:G
15PCCA
DefP:G
15PCCB
DefP:G
15RAB3GAP1
DefP:G
15RERE
DefP:G
15SOX11
DefP:G
15SPTBN4
DefP:G
15TET3
DefP:G
15VPS13B
DefP:G
15ZBTB20
DefP:G
15VAMP2
P:G

vesicle associated membrane protein 2

15SCO2
DefP:G

Intellectual disability

15CDKL5
DefP:G
15CHD2
DefP:G
15CIC
DefP:G
15DCX
DefP:G
15MID1
DefP:G
15SCN2A
DefP:G
15WDR26
DefP:G
15PGAP2
P:G

post-GPI attachment to proteins 2

15PIGO
DefP:G

Intellectual disability

15STX1A
P:G

syntaxin 1A

14WASF1
P:G

WASP family member 1

14SLC6A1
P:G
14SYT1
P:G

synaptotagmin 1

14DDX6
P:G

DEAD-box helicase 6

14PI4KA
P:G
14TDP2
DefP:G

Intellectual disability

14NR4A2
DefP:G

Mild intellectual disability

14CEP152
DefP:G

Intellectual disability

14MED12L
DefP:G

Intellectual disability

13ATM
DefP:R
13NOVA2
DefP:G

Intellectual disability

13MACF1
ModP:G

Severe intellectual disability

13PCDHGC4
P:G

Intellectual disability

13ALDH18A1
DefP:G
13AP3B2
DefP:G
13AP4B1
DefP:G
13ASPM
DefP:G
13BICRA
DefP:G
13CEP104
DefP:G
13CNTNAP2
DefP:G
13CSNK2B
DefP:G
13DNMT3A
DefP:G
13DPF2
DefP:G
13ERLIN2
DefP:G
13FARS2
DefP:G
13FKTN
DefP:G
13FUCA1
DefP:G
13GAN
DefP:G
13HNRNPH2
DefP:G
13IDUA
DefP:G
13MAGEL2
DefP:G
13MAN2B1
DefP:G
13MBOAT7
DefP:G
13MN1
DefP:G
13NEXMIF
DefP:G
13NGLY1
DefP:G
13PEPD
DefP:G
13PEX14
DefP:G
13SETD1B
DefP:G
13SGSH
DefP:G
13TRPM3
DefP:G
13UBE3B
DefP:G
13UNC80
DefP:G
13USP7
DefP:G
13WAC
DefP:G
13ZNF292
DefP:G
13GRIA1
ModP:G

Intellectual disability

13POLR1C
DefP:G

Intellectual disability

13KLHL20
ModP:G

Severe intellectual disability

12ARL13B
DefP:G

Intellectual disability

12CENPF
P:G
12SLC12A6
P:G
12ADGRG1
DefP:G

Intellectual disability

12CLCN6
ModP:G
12POLA1
ModP:G
12TP73
StrP:G
12HDAC4
P:G

Intellectual disability

12NOTCH3
DefP:G

Mild intellectual disability

12MAST3
P:G

Intellectual disability

11GRM1
P:G

Intellectual disability

11ABCC6
DefP:R
11COQ2
DefP:R

Intellectual disability

11CCDC22
ModP:G

Intellectual disability

11TTI1
P:G

Intellectual disability

11AP1B1
DefP:A
11CLCN5
DefP:R
11DLL1
DefP:G

Intellectual disability

11FGD1
DefP:G

Intellectual disability

11NF1
DefP:G

Mild intellectual disability

11NRXN1
DefP:G

Severe intellectual disability

11PQBP1
DefP:G

Intellectual disability

11PRRT2
DefP:A
11SMARCB1
DefP:G

Intellectual disability

11SYN1
DefP:G

Mild intellectual disability

11GMPPB
DefP:G

Mild intellectual disability

11APC2
StrP:G

Intellectual disability

11SLC6A17
ModP:G

Severe intellectual disability

11KIF4A
LimP:G

Intellectual disability

11LRRC7
P:G

Moderate intellectual disability

11TCEAL1
P:G

Intellectual disability

10LONP1
LimP:G

Intellectual disability

10MTFMT
DefP:G

Intellectual disability

10SLC25A15
DefP:G

Severe intellectual disability

10EEFSEC
P:G

Severe intellectual disability

10INPP4A
P:G

Moderate intellectual disability

10BCAS3
P:G
10CAMK4
P:G
10EMC10
P:G
10FMN2
P:G
10KCNK9
P:G
10LARP7
P:G
10MED25
DisP:G
10NARS1
Mod
10SOX4
P:G
10TANGO2
P:G
10TAOK2
P:G
10TBC1D20
P:G
10CSTB
DefP:G

Mild intellectual disability

10ZNF142
P:G

Intellectual disability

10SCN3A
DefP:G

Borderline intellectual disability

10PCYT2
P:G

Intellectual disability

10PAN2
ModP:G

Mild intellectual disability

10PAX1
DefP:A

Moderate intellectual disability

9GABRA3
P:A

Intellectual disability

9ADARB1
P:G

Intellectual disability

9KCNQ5
P:G

Intellectual disability

9KNL1
P:G

Intellectual disability

9ZFX
StrP:G

Moderate intellectual disability

9MYH11
DefSF
9XYLT1
P:G

Intellectual disability

9FBXO22
P:G

Intellectual disability

9ZBTB11
P:A

Moderate intellectual disability

9ABCC9
DefP:G

Mild intellectual disability

9ALDH4A1
DefP:G

Intellectual disability

9CLN8
DefP:G

Intellectual disability

9CYB5R3
DefP:G

Intellectual disability

9DPP6
DisP:R
9ESCO2
DefP:G

Intellectual disability

9FBP1
DefP:R
9FEM1C
LimP:A
9FKRP
DefP:G

Severe intellectual disability

9LAMA2
DefP:G

Intellectual disability

9MTR
DefP:G

Intellectual disability

9NMNAT1
DefP:R
9NPHP4
DefP:R
9PARK7
DefP:R
9PEX1
DefP:G

Intellectual disability

9PEX2
DefP:G

Intellectual disability

9PNKP
DefP:G

Severe intellectual disability

9POMGNT1
DefP:G

Severe intellectual disability

9POMT2
DefP:G

Severe intellectual disability

9SATB1
DefP:G

Intellectual disability

9SPTAN1
DefP:G

Severe intellectual disability

9SYNE1
DefP:R
9TARDBP
DefP:R
9TAT
DefP:G

Intellectual disability

Moderate intellectual disability

9KAT5
P:G

Severe intellectual disability

9IQSEC1
LimP:A

Severe intellectual disability

9BUB1
LimP:G

Intellectual disability

8FEM1B
P:G

Intellectual disability

8INTS11
P:G

Mild intellectual disability

8ALDOA
P:A
8ATG12
P:A
8GLYCTK
ModP:G

Intellectual disability

8SIX3
P:G

Intellectual disability

8TCP1
P:A

Possible

272 genes — click to expand
8CRNKL1
P:G

Severe intellectual disability

8MED16
P:G

Intellectual disability

7TAF13
P:A

Mild intellectual disability

7CEP83
P:G

Intellectual disability

7ABCC1
Lim
7APC
DefSF
7CAPN3
Def
7COL2A1
DefP:R

Intellectual disability

7CORO1A
Def
7ESPN
Def
7GJA8
P:R

Intellectual disability

7HAAO
Def
7KIF1B
LimP:R
7KYNU
Def
7MFN2
Def
7MMUT
Def
7MYRF
Def
7PIK3CD
Def
7PRICKLE1
LimP:R
7RNU4ATAC
DefP:A

Mild intellectual disability

7PUS3
P:G

Profound intellectual disability

7CSTF2
P:A

Mild intellectual disability

7WBP4
P:G

Moderate intellectual disability

7FDXR
DefP:R

Intellectual disability

Intellectual disability

6HOMER2
Mod
6INTS6
P:R
6KIF22
P:R
6KLHL21
P:R
6PLOD1
P:R

Severe intellectual disability

6PRDM16
Str
6PTRH2
P:G

Intellectual disability

6WDR81
P:G

Severe intellectual disability

6WIPI2
P:G

Severe intellectual disability

Intellectual disability

6CCT3
P:A

Intellectual disability

6LSM7
P:A

Intellectual disability

5ZNF407
P:A

Severe intellectual disability

5ALDOB
DefP:R

Intellectual disability

5BCL9
Lim
5BIN1
DefP:R

Mild intellectual disability

5CASZ1
Lim
5CHD1L
Lim
5GALNS
DefP:R

Intellectual disability

5LYST
DefP:R

Intellectual disability

5MEGF10
DefP:R

Intellectual disability

5SBDS
DefP:R

Mild intellectual disability

5TRPV4
DefP:R

Intellectual disability

5VPS13D
Lim
5PNPLA2
Def

Mild intellectual disability

Intellectual disability

Mild intellectual disability

Mild intellectual disability

5HELLS
Mod

Intellectual disability

4FBXO7
P:R

Intellectual disability

4KLF13
Mod

Mild intellectual disability

4FMO5
Dis
4GJA5
Dis
4NPPA
No
4PDP1
P:A

Intellectual disability

4PRKAB2
Dis
4RAD51
P:A

Mild intellectual disability

4TRPS1
P:R

Intellectual disability

4WDR36
Dis

Intellectual disability

3EGF
Lim

Moderate intellectual disability

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