Genes associated with “intellectual disability”

422 genes foundHPO: Intellectual disabilityOpen Targets: Intellectual disability1 PanelApp panel
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

86 genes
1
AHDC1 →

AT-hook DNA binding motif containing 1

59
score
ClinGen: DefinitivePanel: Green ↑GTR ↑

Moderate intellectual disability

Frequency
62%
n=13
P/LP Variants
135
OT Score
0.71
2
MED13L →

mediator complex subunit 13L

48
score
ClinGen: DefinitivePanel: Green ↑GTR ↑
Frequency
-
P/LP Variants
1
OT Score
0.67
46
score
ClinGen: DefinitivePanel: Green ↑GTR ↑

Intellectual disability

Frequency
100%
n=23
P/LP Variants
1
OT Score
-
4
QRICH1 →

glutamine rich 1

45
score
ClinGen: DefinitivePanel: Green ↑GTR ↑

Intellectual disability

Frequency
100%
n=3
P/LP Variants
6
OT Score
0.57
43
score
ClinGen: DefinitivePanel: Green ↑GTR ↑
Frequency
-
P/LP Variants
5
OT Score
-
6
SLC6A8 →

solute carrier family 6 member 8

42
score
ClinGen: DefinitivePanel: Green ↑GTR ↑
Frequency
-
P/LP Variants
7
OT Score
0.62
7
ZMYND11 →

zinc finger MYND-type containing 11

40
score
ClinGen: DefinitivePanel: Green ↑GTR ↑

Mild intellectual disability

Frequency
100%
n=7
P/LP Variants
62
OT Score
0.59
40
score
ClinGen: DefinitivePanel: Green ↑GTR ↑

Severe intellectual disability

Frequency
100%
n=19
P/LP Variants
1
OT Score
-
39
score
ClinGen: DefinitivePanel: Green ↑GTR ↑
Frequency
-
P/LP Variants
8
OT Score
-
39CTCF
DefP:G

CCCTC-binding factor

39BRWD3
DefP:G

Intellectual disability

39POGZ
DefP:G

pogo transposable element derived with ZNF domain

38DDX3X
DefP:G

DEAD-box helicase 3 X-linked

38KMT2C
DefP:G

lysine methyltransferase 2C

38CHD5
P:G

Intellectual disability

37DYRK1A
DefP:G

Severe intellectual disability

36CASK
DefP:G

Moderate intellectual disability

35POU3F3
DefP:G

Intellectual disability

35MYT1L
DefP:G

myelin transcription factor 1 like

35PURA
DefP:G

purine rich element binding protein A

35ASH1L
DefP:G

Intellectual disability

34MECP2
DefP:G

Mild intellectual disability

34BCAP31
DefP:G

Severe intellectual disability

33OPHN1
DefP:G
33SMS
DefP:G
33HUWE1
DefP:G

Intellectual disability

32TCF20
DefP:G

transcription factor 20

31MTOR
DefP:G

Intellectual disability

31SETD2
DefP:G

SET domain containing 2, histone lysine methyltransferase

31RAC1
DefP:G
31UPF3B
DefP:G

Intellectual disability

31MEIS2
DefP:G

Intellectual disability

31ATRX
DefP:G

Intellectual disability

30TRIO
DefP:G
30TUBA1A
DefP:G

tubulin alpha 1a

30TELO2
DefP:G

Intellectual disability

30PIDD1
DefP:G

p53-induced death domain protein 1

30BCL11A
DefP:G

BCL11 transcription factor A

30CREBBP
DefP:G

Intellectual disability

29ASXL3
DefP:G
28TANC2
DefP:G

Intellectual disability

28SMARCA2
DefP:G
28ITPR1
DefP:G

Severe intellectual disability

27SLC2A1
DefP:G

solute carrier family 2 member 1

27DHCR7
DefP:G
27OFD1
DefP:G#7

Profound intellectual disability

26RPS6KA3
DefP:G#17
26CACNA1C
DefP:G
26PIGL
DefP:G

Intellectual disability

26MCPH1
DefP:G

Intellectual disability

25PAH
DefP:G
25DLD
DefP:G
25ANKRD11
DefP:G
25CDK13
DefP:G
25DLG3
DefP:G
25NSUN2
DefP:G
25SETD5
DefP:G
25USP9X
DefP:G
25TCF4
DefP:G
25EP300
DefP:G#14
24UBE2A
DefP:G

Intellectual disability

24IKBKG
DefP:G#19
24FGFR3
DefP:R#1

Severe intellectual disability

24HGSNAT
DefP:G

Intellectual disability

24GLI3
DefP:A
24STX1A
P:G

syntaxin 1A

23HEPACAM
DefP:G

Intellectual disability

23PTPN11
DefP:G
23ELN
DefP:R#3
23PTEN
DefSFP:G#4

Intellectual disability

23OCRL
DefP:G
22TWIST1
DefP:G
22AP1S2
DefP:G

Severe intellectual disability

22GAMT
DefP:G

Intellectual disability

22BCOR
DefP:G
22SHANK3
DefP:G
21NFIX
DefP:G
21CEP290
DefP:G
21CTNNB1
DefP:G
21GRIN2B
DefP:G
21L1CAM
DefP:G
21MEF2C
DefP:G
21SETBP1
DefP:G
20PIK3CA
RefP:G#16

Mild intellectual disability

20SATB2
DefP:G

SATB homeobox 2

20STXBP1
DefP:G

syntaxin binding protein 1

Consider

217 genes
20KMT2E
DefP:G

lysine methyltransferase 2E (inactive)

20KANSL1
DefP:G

KAT8 regulatory NSL complex subunit 1

19NBEA
DefP:G

neurobeachin

19SPG11
DefP:G

Intellectual disability

19SYT1
P:G

synaptotagmin 1

19MLC1
DefP:G

Mild intellectual disability

19CBS
DefP:G
19GPC3
DefP:G
19IDUA
DefP:G
19MAN2B1
DefP:G
19PCCA
DefP:G
19PCCB
DefP:G
19PMM2
DefP:G
19TAT
DefP:G
19TRIP12
DefP:G
19VPS13B
DefP:G
19CAMK2A
DefP:G

calcium/calmodulin dependent protein kinase II alpha

19PAK3
DefP:G

Intellectual disability

19GABRB2
DefP:G

gamma-aminobutyric acid type A receptor subunit beta2

19PPP2R5D
DefP:G

protein phosphatase 2 regulatory subunit B'delta

19ARFGEF1
DefP:G

ARF guanine nucleotide exchange factor 1

19CAMK2B
P:G

calcium/calmodulin dependent protein kinase II beta

18FGFR2
DefP:A#5

Moderate intellectual disability

18PACS1
DefP:G

phosphofurin acidic cluster sorting protein 1

18YY1
DefP:G

YY1 transcription factor

18SYP
ModP:G

Intellectual disability

18FGFR1
DefP:R
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

17ARID1B
DefP:G
17ASXL1
DefP:G
17CHD8
DefP:G
17FRMPD4
DefP:G

FERM and PDZ domain containing 4

17KCNQ2
DefP:G
17KMT2A
DefP:G
17SON
DefP:G
17SHOC2
DefP:G

Intellectual disability

17ZBTB20
DefP:G

Intellectual disability

17DNMT3A
DefP:G
17MMAA
DefP:G
17GRIK2
DefP:G

Intellectual disability

17RBBP8
P:G

Intellectual disability

16ASAH1
DefP:G

Intellectual disability

16LRP2
No P:G
16MED23
ModP:G
16SLC12A6
P:G
16EBF3
DefP:G

Intellectual disability

16PEX7
DefP:G

Intellectual disability

16KCNN2
P:G

potassium calcium-activated channel subfamily N member 2

15ARF3
P:G

ARF GTPase 3

15KDM5A
LimP:G

lysine demethylase 5A

15SERAC1
DefP:G

Intellectual disability

15CEP104
DefP:G
15DDX11
DefP:G
15DEPDC5
DefP:G
15IQSEC2
DefP:G
15LZTR1
DefSFP:G
15SETD1B
DefP:G
15LAMP2
DefP:G

Intellectual disability

15VAMP2
P:G

vesicle associated membrane protein 2

15SCO2
DefP:G

Intellectual disability

15ARID2
DefP:G
15ATM
DefP:R
15CAMTA1
DefP:G
15CNOT1
DefP:G
15HDAC8
DefP:G
15KMT2D
DefP:G
15NR4A2
DefP:G
15OTC
DefSFP:G
15SHH
DefP:G
15SMC1A
DefP:G
15SYNGAP1
DefP:G
15PGAP2
P:G

post-GPI attachment to proteins 2

15LIMK1
P:R
15USP27X
ModP:A

ubiquitin specific peptidase 27 X-linked

14ANK3
ModP:G

Intellectual disability

14RAB3GAP2
DefP:G

Severe intellectual disability

14PPP1R12A
StrP:G
14DDX6
P:G

DEAD-box helicase 6

14CCND2
DefP:G

Severe intellectual disability

14CENPF
P:G
14KCNH5
DefP:G

Intellectual disability

14KMT5B
DefP:G

Intellectual disability

13PMPCA
DefP:A

Intellectual disability

13MACF1
ModP:G

Severe intellectual disability

ARTHROGRYPOSIS, CLEFT PALATE, CRANIOSYNOSTOSIS, AND IMPAIRED INTELLECTUAL DEVELOPMENT; ACCIID

13ALMS1
DefP:G

ALOPECIA-INTELLECTUAL DISABILITY SYNDROME 1; APMR1

Alopecia-intellectual disability syndrome 2

Alopecia-intellectual disability syndrome 3

ALOPECIA-INTELLECTUAL DISABILITY SYNDROME 4; APMR4

13BICRA
DefP:G
13CC2D1A
DefP:G
13COG6
DefP:G
13COL4A1
DefP:G

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

DEVELOPMENTAL DELAY WITH VARIABLE INTELLECTUAL DISABILITY AND DYSMORPHIC FACIES; DIDDF

13GNAO1
DefP:G
13HNRNPU
DefP:G

INTELLECTUAL DISABILITY AND MYOPATHY SYNDROME; IDMYS

13IRF2BPL
DefP:G
13IVD
DefP:G
13KCNQ3
DefP:G
13LAMA1
P:G
13MMUT
Def
13MN1
DefP:G

INTELLECTUAL DEVELOPMENTAL DISORDER, AUTOSOMAL RECESSIVE 65; MRT65

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

13POLR3B
DefP:G
13PPP1R21
DefP:G
13RAB3GAP1
DefP:G
13RARB
DefP:G

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

13SGSH
DefP:G
13TBC1D24
DefP:G
13THOC6
DefP:G
13TRMU
Def
13UNC80
DefP:G
13WDR62
DefP:G

INTELLECTUAL DEVELOPMENTAL DISORDER, X-LINKED 1; XLID1

13ZEB2
DefP:G
13ZMIZ1
DefP:G
13ZMYM2
DefP:G
12MLYCD
DefP:G

Intellectual disability

12NF1
DefP:G

Intellectual disability

12UBE3B
DefP:G

Severe intellectual disability

12PPFIBP1
P:G

Intellectual disability

12DYNC1H1
DefP:G

Intellectual disability

12FKBP6
P:R
12EED
ModP:G
12ELP1
Mod
12AP4B1
DefP:G

Severe intellectual disability

12THUMPD1
P:G

Intellectual disability

12FRRS1L
DefP:A

Severe intellectual disability

11CDH11
DefP:G

Mild intellectual disability

11CCDC22
ModP:G

Intellectual disability

11TNPO2
P:G

Intellectual disability

11PAN2
ModP:G

Moderate intellectual disability

11CAPN3
Def
11EYA1
DefP:R
11LARS2
DefP:A
11LMX1B
DefP:R
11NRXN1
DefP:G

Severe intellectual disability

11PQBP1
DefP:G

Intellectual disability

11RAI1
DefP:G

Mild intellectual disability

11SOX5
DefP:G

Intellectual disability

11TBX4
DefP:R
11TCF12
DefP:R
11ZNF462
DefP:G

Mild intellectual disability

11KIF4A
LimP:G

Intellectual disability

11AP3B1
DefP:G

Mild intellectual disability

11COQ4
DefP:G

Moderate intellectual disability

11GABRA1
DefP:G

Severe intellectual disability

11UNC13A
DefP:G

Moderate intellectual disability

11TCEAL1
P:G

Intellectual disability

10LONP1
LimP:G

Intellectual disability

10SLC25A15
DefP:G

Severe intellectual disability

10COLEC11
P:G
10LARP7
P:G
10PI4KA
P:G
10SOX4
P:G
10TAF1
P:G
10TTI2
P:G
10ZFHX3
P:G
10ATAD3A
P:G

Intellectual disability

10FBXW11
P:G

Intellectual disability

10ZNF142
P:G

Intellectual disability

Intellectual disability

10FMN2
P:G

Intellectual disability

10PCYT2
P:G

Intellectual disability

10PTDSS1
P:G

Intellectual disability

10SUPT16H
P:G

Intellectual disability

10PNPLA6
DefP:G

Intellectual disability

10DCC
DefP:A

Intellectual disability

9AP1B1
DefP:A

Intellectual disability

Severe intellectual disability

9GRID2
P:G

Intellectual disability

9PDZD8
P:G

Intellectual disability

9SEL1L
P:G

Severe intellectual disability

9TAF6
P:G

Intellectual disability

9ZFX
StrP:G

Moderate intellectual disability

9ABCC9
DefP:G

Mild intellectual disability

9ALDH4A1
DefP:G

Intellectual disability

9ARFGEF2
DefP:G

Severe intellectual disability

9ATP1A2
DefP:G

Intellectual disability

9COL1A2
DefP:R
9DKC1
DefP:G

Intellectual disability

9DPAGT1
DefP:G

Intellectual disability

9ETHE1
DefP:G

Intellectual disability

9GLDC
DefP:G

Intellectual disability

9IFT172
DefP:G

Intellectual disability

9NANS
DefP:G

Intellectual disability

9PKD1
Def
9RAB23
DefP:G

Intellectual disability

9SYNE1
DefP:R
9TRIM37
DefP:R
9VPS11
DefP:G

Intellectual disability

Intellectual disability

Profound intellectual disability

8CEP135
P:G

Severe intellectual disability

8COASY
P:G

Intellectual disability

8EIF4A2
P:G

Mild intellectual disability

8HYCC1
Def

Intellectual disability

8RUBCN
P:R
8RMRP
DefP:A

Intellectual disability

8PRMT7
P:G

Mild intellectual disability

8GTF2I
P:A
8PLAT
DisP:A
8SLC35A1
ModP:G

Intellectual disability

8SPAST
P:G

Intellectual disability

8ST3GAL3
ModP:G

Intellectual disability

Possible

94 genes — click to expand
8OTX2
P:G

Severe intellectual disability

8KCNC2
Def

Intellectual disability

Severe intellectual disability

8CDK19
P:G

Intellectual disability

7ALG14
LimP:A

Severe intellectual disability

7ANK1
Def
7CEP164
Def
7F11
Def
7FBN1
DefSFP:R

Mild intellectual disability

7GBA2
DefP:A

Intellectual disability

7IKBKB
Def
7KYNU
Def
7MYO15A
Def
7PIEZO1
Def
7RPL5
Def
7GTF3C3
P:G

Mild intellectual disability

7WBP4
P:G

Moderate intellectual disability

7NARS1
Mod

Intellectual disability

7FDXR
DefP:R

Profound intellectual disability

6HS2ST1
P:A

Intellectual disability

6CHMP1A
P:G

Intellectual disability

6GTF2E2
P:G

Moderate intellectual disability

6LETM1
P:G

Severe intellectual disability

6NTNG2
P:G

Intellectual disability

6OSGEP
P:G

Intellectual disability

Severe intellectual disability

6RUNX2
P:R

Profound intellectual disability

6SMOC1
P:G

Intellectual disability

6SNAP29
P:G

Severe intellectual disability

6WIPI2
P:G

Severe intellectual disability

6H4C5
Str

Intellectual disability

6WFS1
DefP:R

Intellectual disability

6CCT3
P:A

Intellectual disability

Severe intellectual disability

5VARS1
Def

Intellectual disability

5BAIAP2
P:A

Severe intellectual disability

Mild intellectual disability

5AGPAT2
DefP:R

Intellectual disability

5BRCA1
DefSFP:R

Intellectual disability

5CDT1
DefP:R

Intellectual disability

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

5WDR35
DefP:R

Intellectual disability

Mild intellectual disability

5PRORP
Def

Intellectual disability

5MTHFD1
Def

Mild intellectual disability

Mild intellectual disability

4FBXO7
P:R

Intellectual disability

4IFT74
Def

Intellectual disability

4BGN
StrP:R

Intellectual disability

4DAP3
P:A

Intellectual disability

4SRP54
P:A

Mild intellectual disability

4TDP1
P:A

Intellectual disability

4TRPS1
P:R

Intellectual disability

4MARS1
Mod

Intellectual disability

3ANTXR2
Def

Intellectual disability

Intellectual disability

3GJA1
LimP:R

Intellectual disability

3GUCY2D
Def

Intellectual disability

3LIFR
Def

Intellectual disability

3MSTO1
Def

Mild 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.