Genes associated with “intellectual disability

791 genes foundHPO: Intellectual disability1 PanelApp panel
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

103 genes
46
score
ClinGen: DefinitivePanel: GreenGTR ↑

Intellectual disability

Frequency
100%
n=5
P/LP Variants
3
OT Score
-
45
score
ClinGen: DefinitivePanel: GreenGTR ↑

Intellectual disability

Frequency
100%
n=16
P/LP Variants
5
OT Score
-
44
score
ClinGen: DefinitivePanel: GreenGTR ↑

Moderate intellectual disability

Frequency
62%
n=13
P/LP Variants
2
OT Score
-
44
score
ClinGen: DefinitivePanel: GreenGTR ↑

Moderate intellectual disability

Frequency
-
P/LP Variants
6
OT Score
-
43
score
ClinGen: DefinitivePanel: GreenGTR ↑
Frequency
-
P/LP Variants
8
OT Score
-
41
score
ClinGen: DefinitivePanel: GreenGTR ↑
Frequency
-
P/LP Variants
5
OT Score
-
40
score
ClinGen: DefinitivePanel: GreenP2G #14GTR ↑

Intellectual disability

Frequency
100%
n=8
P/LP Variants
4
OT Score
-
39
score
ClinGen: DefinitivePanel: GreenP2G #21GTR ↑

Intellectual disability

Frequency
100%
n=8
P/LP Variants
4
OT Score
-
39
score
ClinGen: DefinitivePanel: GreenGTR ↑
Frequency
-
P/LP Variants
6
OT Score
-
39ATRX
DefP:G

Intellectual disability

38GATAD2B
DefP:G
38MED12
DefP:G
38USP9X
DefP:G
37FOXP1
DefP:G
37NAA15
DefP:G
35ADNP
DefP:G
35BRWD3
DefP:G
35POGZ
DefP:G
34TELO2
DefP:G

Intellectual disability

34TRIP12
DefP:G

Intellectual disability

34PHF8
DefP:G

Mild intellectual disability

33KMT2C
DefP:G

Intellectual disability

33CTCF
DefP:G
33KIF11
DefP:G
33OPHN1
DefP:G
33ZDHHC9
DefP:G
33HUWE1
DefP:G

Intellectual disability

32GNB1
DefP:G
31RAC1
DefP:G
31SETD5
DefP:G
30MECP2
DefP:G

Profound intellectual disability

30TRIO
DefP:G
30KAT6B
DefP:G
30CHD2
DefP:G

Intellectual disability

29RPS6KA3
DefP:G#17

Intellectual disability

29KIF1A
DefP:G
28TANC2
DefP:G

Intellectual disability

28OFD1
DefP:G#7
28ATP8A2
DefP:G
28FGFR3
DefP:R#1
28KMT2A
DefP:G
28PGAP3
DefP:G
28TRAPPC9
DefP:G
28TCF4
DefP:G
28TBL1XR1
DefP:G
27CHD4
DefP:G
27CNNM2
DefP:G
27UBE2A
DefP:G
27ARID2
DefP:G

Intellectual disability

27ASH1L
DefP:G

Intellectual disability

27ZMYND11
DefP:G

Mild intellectual disability

26IKBKG
DefP:G#19
26CACNA1C
DefP:G
26PIGL
DefP:G

Intellectual disability

26SHANK3
DefP:G
26MCPH1
DefP:G

Intellectual disability

25RAI1
DefP:G

Mild intellectual disability

25ANKRD11
DefP:G
25ARID1B
DefP:G
25BCL11B
DefP:G
25GRIN2B
DefP:G
25KMT2D
DefP:G
25NONO
DefP:G
25RTN4IP1
DefP:G
25UBE3A
DefP:G
25KRAS
DefP:G#15
24SLC2A1
DefP:G
24KDM5B
ModP:G
24ASXL1
DefP:G

Profound intellectual disability

24SLC6A8
DefP:G
24EZH2
DefP:G
24NFIX
DefP:G
23ITPR1
DefP:G

Moderate intellectual disability

23ARID1A
DefP:G
23CNKSR2
DefP:G
23CTNNB1
DefP:G
23DYRK1A
DefP:G
23MYT1L
DefP:G
23ZBTB18
DefP:G
23HPRT1
DefP:G
23CSNK2B
DefP:G
23HEPACAM
DefP:G

Intellectual disability

23SMARCA4
DefP:G
22PAH
DefP:G

Intellectual disability

22PPP2R1A
DefP:G
22SPG11
DefP:G

Intellectual disability

22ARG1
DefP:G
21GRIK2
DefP:G

Intellectual disability

21ANKRD17
DefP:G
21KDM5C
DefP:G
21MEF2C
DefP:G
21SET
DefP:G

Intellectual disability

21SETBP1
DefP:G
21DHCR7
DefP:G
21AKT3
DefP:G

Intellectual disability

20VPS13B
DefP:G

Intellectual disability

20HIVEP2
P:G
20EBF3
DefP:G
20SETD2
DefP:G
20SYNGAP1
DefP:G
20WDR26
DefP:G
20H1-4
Def
20LRP2
No P:G

Consider

259 genes
20QRICH1
DefP:G

Intellectual disability

20NUS1
DefP:G

Intellectual disability

20UBE3B
DefP:G

Severe intellectual disability

20GLI3
DefP:A
19RAB3GAP2
DefP:G

Severe intellectual disability

19CAMTA1
DefP:G
19CIC
DefP:G
19KANSL1
DefP:G
19KDM6A
DefP:G
19KMT2E
DefP:G
19L1CAM
DefP:G
19NR2F1
DefP:G
18FGFR2
DefP:A#5

Moderate intellectual disability

18IDUA
DefP:G
17BCL11A
DefP:G
17CHD8
DefP:G
17DCX
DefP:G
17KCNQ2
DefP:G
17MID1
DefP:G
17PHIP
DefP:G
17SATB2
DefP:G
17SLC9A6
DefP:G
17SON
DefP:G
17SHOC2
DefP:G

Intellectual disability

17DYNC1H1
DefP:G

Intellectual disability

17AGA
DefP:G
17COL4A1
DefP:G
17GNAO1
DefP:G
17GRIN1
DefP:G
17GRIN2A
DefP:G
17IRF2BPL
DefP:G
17KMT2B
DefP:G
17LZTR1
DefSFP:G
17MBD5
DefP:G
17NAGLU
DefP:G
17ASL
DefP:G

Intellectual disability

16ASAH1
DefP:G

Intellectual disability

16LINS1
DefP:G
16MED23
ModP:G
16OGT
ModP:G
16PIGO
DefP:G
16HDAC4
P:G
16MBOAT7
DefP:G

Intellectual disability

16PAX6
DefP:R
15GLB1
DefP:G

Mild intellectual disability

15CAMK2A
DefP:G

Intellectual disability

15AP4B1
DefP:G
15ASPM
DefP:G
15ATN1
DefP:G
15DNMT3A
DefP:G
15HNF1B
DefP:A
15HNRNPU
DefP:G
15SETD1B
DefP:G
15SGSH
DefP:G
15SOX11
DefP:G
15TET3
DefP:G
15THOC2
DefP:G
15TLK2
DefP:G
15WAC
DefP:G
15ZBTB20
DefP:G
15EFTUD2
DefP:G
15FOXG1
DefP:G
15GPC3
DefP:G
15LMNB1
DefP:G
15PBX1
DefP:G
15SCN2A
DefP:G
15STXBP1
DefP:G
15MAN1B1
DefP:G

Moderate intellectual disability

15PLP1
DefP:G

Intellectual disability

15ARMC9
DefP:G

Intellectual disability

14ANK3
ModP:G

Intellectual disability

14PPP1R12A
StrP:G
14NDUFA10
ModP:R
14TBC1D20
P:G

Profound intellectual disability

14YAP1
P:R

Intellectual disability

14CCND2
DefP:G

Severe intellectual disability

14TRA2B
DefP:G

Intellectual disability

14MTOR
DefP:G

Intellectual disability

14DPF2
DefP:G

Intellectual disability

14TRAPPC4
DefP:G

Profound intellectual disability

13PIK3R1
DefP:R

Mild intellectual disability

13FANCC
DefP:A

Intellectual disability

13ATM
DefP:R
13CLCN5
DefP:R
13CLPB
LimP:G
13PRRT2
DefP:A
13PMPCA
DefP:A

Intellectual disability

13NDE1
DefP:G

Profound intellectual disability

13TRAPPC6B
DefP:G

Severe intellectual disability

13MACF1
ModP:G

Severe intellectual disability

13MAP1B
StrP:G

Intellectual disability

13ABCC9
DefP:G
13ACTG1
DefP:G

ALOPECIA-INTELLECTUAL DISABILITY SYNDROME 1; APMR1

Alopecia-intellectual disability syndrome 2

Alopecia-intellectual disability syndrome 3

ALOPECIA-INTELLECTUAL DISABILITY SYNDROME 4; APMR4

13ATP1A1
DefP:G
13B3GLCT
DefP:G
13B9D1
DefP:G
13BICRA
DefP:G
13CACNA1D
DefP:G
13CAMK2B
P:G
13CBS
DefP:G

CLEFT PALATE, CARDIAC DEFECTS, AND IMPAIRED INTELLECTUAL DEVELOPMENT; CPCMR

13D2HGDH
DefP:G
13DDX11
DefP:G

DEVELOPMENTAL DELAY WITH VARIABLE INTELLECTUAL DISABILITY AND DYSMORPHIC FACIES; DIDDF

13EEF1A2
DefP:G
13EHMT1
DefP:G
13ELP2
DefP:G
13ERLIN2
DefP:G
13FRMPD4
DefP:G
13GNAI1
DefP:G

INTELLECTUAL DISABILITY AND MYOPATHY SYNDROME; IDMYS

13KCNC1
DefP:G
13KIDINS220
DefP:G
13KMT5B
DefP:G
13KPTN
DefP:G
13LAMA1
P:G
13MAGEL2
DefP:G
13MAPK8IP3
DefP:G
13MMAA
DefP:G

INTELLECTUAL DEVELOPMENTAL DISORDER, AUTOSOMAL RECESSIVE 65; MRT65

INTELLECTUAL DISABILITY-HYPOTONIC FACIES SYNDROME, X-LINKED, 1; MRXHF1

INTELLECTUAL DEVELOPMENTAL DISORDER, X-LINKED, SYNDROMIC, SNIJDERS BLOK TYPE; MRXSSB

13PCCB
DefP:G
13PEX13
DefP:G
13PMM2
DefP:G
13RERE
DefP:G

SHORT STATURE, BRACHYDACTYLY, IMPAIRED INTELLECTUAL DEVELOPMENT, AND SEIZURES; SBIDDS

13SDCCAG8
DefP:G
13SKI
DefP:G
13SMARCC2
DefP:G
13SPTAN1
DefP:G
13WARS2
DefP:G
13WDPCP
DefP:G
13WDR62
DefP:G

INTELLECTUAL DEVELOPMENTAL DISORDER, X-LINKED 1; XLID1

13DTYMK
P:G

Intellectual disability

13PRUNE1
P:G

Profound intellectual disability

13OTUD5
ModP:G

Intellectual disability

12MLYCD
DefP:G

Intellectual disability

12NF1
DefP:G

Intellectual disability

12SMCHD1
DefP:R

Intellectual disability

12HECW2
DefP:G

Intellectual disability

12SUFU
DefP:G

Mild intellectual disability

12TIMM50
DefP:G

Severe intellectual disability

12CENPF
P:G
12INPP5K
P:G
12PI4KA
P:G
12TAOK2
P:G
12SCN8A
DefP:G

Profound intellectual disability

12SOX2
P:G
12TGIF1
P:G
12ATP2B1
P:G

Intellectual disability

12DDX59
LimP:G

Intellectual disability

12KCNT1
DefP:G

Intellectual disability

12POLR3B
DefP:G

Mild intellectual disability

11SETD1A
P:G

Intellectual disability

11CDH11
DefP:G

Mild intellectual disability

11PNP
DefP:R

Intellectual disability

11VPS53
P:G

Intellectual disability

11CDH15
DisP:R
11SPG7
DefP:R
11CCDC22
ModP:G

Intellectual disability

11AGXT
DefP:A
11BUB1
LimP:G
11GCH1
DefP:G

Intellectual disability

11LRP5
DefP:A
11MYCN
DefP:G

Intellectual disability

11OTUD7A
LimP:G
11PCDH19
DefP:G

Intellectual disability

11KIF4A
LimP:G

Intellectual disability

11COQ4
DefP:G

Moderate intellectual disability

11ELOVL4
DefP:G

Profound intellectual disability

11LARGE1
DefP:G

Profound intellectual disability

11MANBA
DefP:G

Intellectual disability

11NAGA
DefP:G

Mild intellectual disability

11NOTCH3
DefP:G

Severe intellectual disability

11UNC13A
DefP:G

Severe intellectual disability

10IRX5
ModP:G

Intellectual disability

10KLHL20
ModP:G

Mild intellectual disability

10ALDOA
P:A
10TRPS1
P:R
10GPC4
P:G

Intellectual disability

10ERCC8
DefP:G

Intellectual disability

10BRF1
P:G

Intellectual disability

10EEFSEC
P:G

Severe intellectual disability

10ALDH3A2
P:G
10CAMK4
P:G
10CDT1
DefP:R

Intellectual disability

10EMC10
P:G
10EPB41L3
P:G
10FBXL3
P:G
10FMN2
P:G
10KCNN2
P:G
10LARP7
P:G
10LRRC7
P:G
10PGAP1
P:G
10PGAP2
P:G
10PTPN4
P:G
10SOX4
P:G
10STEEP1
Mod
10SUPT16H
P:G
10TAF1
P:G
10TANGO2
P:G
10TECPR2
P:G
10UGP2
P:G
10USP27X
ModP:A
10ZFHX3
P:G
10ATAD3A
P:G

Intellectual disability

Intellectual disability

Intellectual disability

10PCYT2
P:G

Intellectual disability

10PTDSS1
P:G

Intellectual disability

10COLEC11
P:G

Intellectual disability

10HPD
DefP:G

Mild intellectual disability

10PNPLA6
DefP:G

Intellectual disability

9PDZD8
P:G

Intellectual disability

9SEL1L
P:G

Severe intellectual disability

Intellectual disability

9CAPN3
Def
9CORO1A
Def

Intellectual disability

9ACSF3
DefP:R
9AFG3L2
DefP:R
9AHCY
DefP:G

Intellectual disability

9ALX4
DefP:A

Intellectual disability

9ATP1A2
DefP:G

Intellectual disability

9BRAT1
DefP:G

Intellectual disability

9COL6A3
DefP:R
9DKC1
DefP:G

Intellectual disability

9DPAGT1
DefP:G

Intellectual disability

9ETHE1
DefP:G

Intellectual disability

9FEM1C
LimP:A
9GALNS
DefP:R
9GLDC
DefP:G

Intellectual disability

9IFT172
DefP:G

Intellectual disability

9PSAT1
DefP:R
9SPR
DefP:G

Intellectual disability

9TRPM1
DefP:R
9TUBGCP6
DefP:G

Intellectual disability

9USP34
LimP:A
9MAST1
P:G

Intellectual disability

9TTI2
P:G

Severe intellectual disability

Intellectual disability

9TOR1A
P:G

Severe intellectual disability

8HERC1
P:G

Intellectual disability

8KIF22
P:R
8PRMT7
P:G

Mild intellectual disability

8AGAP1
P:A
8ATG12
P:A
8KIF5B
P:A
8ST3GAL3
ModP:G

Profound intellectual disability

8TWIST2
P:A

Possible

405 genes — click to expand

Severe intellectual disability

8CANT1
DefP:R

Intellectual disability

7CHRNA7
Ref

Moderate intellectual disability

7AFG2A
Def
7APC
DefSF
7COX20
Def
7DCC
DefP:A

Mild intellectual disability

7FAN1
Def
7FLCN
Def
7FRAS1
DefP:A

Intellectual disability

7LPIN2
Def
7MERTK
Def
7MYO15A
Def
7NDUFS6
Def
7NDUFV2
Def
7OPN1LW
Def
7PIEZO1
Def
7RBCK1
Def
7UBE3C
P:A

Severe intellectual disability

7WBP4
P:G

Moderate intellectual disability

7COL18A1
DefP:R

Intellectual disability

6HS2ST1
P:A

Intellectual disability

6WASHC4
P:A

Profound intellectual disability

6ANAPC1
Mod
6CAPN10
P:R
6DDHD2
P:G

Intellectual disability

6FLII
Mod
6INTS6
P:R
6KIF26B
P:R
6KLF13
Mod
6MC2R
P:R
6NLRP3
P:R
6PIEZO2
P:R
6PISD
ModP:A

Intellectual disability

6PLPBP
P:G

Intellectual disability

6REL
Mod
6RNU4-2
Str
6STRADA
P:G

Intellectual disability

6TFB2M
P:R
6VRK1
P:G

Intellectual disability

6WSB2
P:A

Moderate intellectual disability

5VARS1
Def

Intellectual disability

5BAIAP2
P:A

Severe intellectual disability

5AGPAT2
DefP:R

Intellectual disability

5ATPAF2
Lim
5BRCA1
DefSFP:R

Intellectual disability

5COL6A1
DefP:R

Intellectual disability

5CTNS
DefP:R

Intellectual disability

EPILEPSY, X-LINKED 1, WITH VARIABLE LEARNING DISABILITIES AND BEHAVIOR DISORDERS; EPILX1

5EVC2
DefP:R

Intellectual disability

5FAM111A
DefP:R

Intellectual disability

5GRAP
Lim
5MIEF2
Lim
5MSX2
DefP:R

Intellectual disability

5NSMCE3
Lim
5PDCD1
Lim
5TJP1
Lim
5VPS13D
Lim
5WDR35
DefP:R

Intellectual disability

Intellectual disability

5KCNC2
Def

Severe intellectual disability

5MTHFD1
Def

Mild intellectual disability

4FBXO7
P:R

Intellectual disability

4IGBP1
DisP:R

Intellectual disability

4IFT74
Def

Intellectual disability

4DAP3
P:A

Intellectual disability

4MYOM1
Dis
4SLC5A5
P:A

Intellectual disability

4SRP54
P:A

Mild intellectual disability

4WDR36
Dis
4MAP3K7
P:R

Mild intellectual disability

3CRPPA
Def

Profound intellectual disability

Intellectual disability

3MSTO1
Def

Mild intellectual disability

3MTRFR
Def

Intellectual disability

3POR
Def

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.