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Table 1 Details of known NS-ID genes, as well as S-ID genes where allelic variants cause NS-ID, including the types of mutations found to cause disease and mode of inheritance

From: The genetic basis of non-syndromic intellectual disability: a review

Gene Name

OMIM Ref

X-linked/Autosomal (MR/ID)

Cytogenetic Banda

Phenotypic Expression*

Mutation Type

Reference

ACSL4

300157

X-linked (MRX63 & 68)

Xq22.3

Males: MR

Missense, splice site

(Meloni et al. 2002)

Females: Variable

AFF2/FMR2

300806

X-linked

Xq28

Dominantb

5′ GGC repeat amplification leading to methylation

(Gecz et al. 1996)

AGTR2

300034

X-linked (MRX88)

Xq23

Recessive

Missense, Truncating

(Vervoort et al. 2002)

AP1S2

300629

X-linked (MRX59)

Xp22.2

Recessive

Truncating

(Tarpey et al. 2006)

ARHGEF6

300267

X-linked (MRX46)

Xq26.3

Recessive

Splice site

(Kutsche et al. 2000)

ARX

300382

X-linked

Xp21.3

Males: MR; Females: Low-normal IQ

In frame insertions/deletions, missense

(Bienvenu et al. 2002; Stromme et al. 2002a, b; Troester et al. 2007)

ATRX

300032

X-linked

Xq21.1

Recessive

Missense

(Yntema et al. 2002)

BRWD3

300553

X-linked (MRX93)

Xq21.1

Recessive

Missense, frame-shift

(Field et al. 2007)

CASK

300172

X-linked

Xp11.4

Recessive

Missense

(Tarpey et al. 2009; Hackett et al. 2009)

CC2D1A

610055

Autosomal (MRT3)

19p13.12

Recessive

Truncating

(Basel-Vanagaite et al. 2006)

CDH15

114019

Autosomal (MRD3)

16q24.3

Dominant

Missense

(Bhalla et al. 2008)

CRBN

609262

Autosomal (MRT2)

3p26.3

Recessive

Truncating

(Higgins et al. 2004)

DLG3

300189

X-linked (MRX90)

Xq13.1

Males: MR

Truncating

(Tarpey et al. 2004)

Females: Variable

DOCK8

611432

Autosomal (MRD2)

9p24.3

Dominant

Deletion, translocation

(Griggs et al. 2008)

FGD1

305400

X-linked

Xp11.22

Recessive

Missense

(Lebel et al. 2002)

FTSJ1

300499

X-linked (MRX9 & 44)

Xp11.23

Recessive

Truncating, missense

(Freude et al. 2004)

GDI1

300104

X-linked (MRX41 & 48)

Xq28

Dominantb

Truncating, missense

(D’Adamo et al. 1998; (Bienvenu et al. 1998)

GRIK2

138244

Autosomal (MRT6)

6q21

Recessive

Truncating

(Motazacker et al. 2007)

HUWE1

300697

X-linked (MRXS-Turner & MRX17)

Xp11.22

Recessive

Missense, microduplication

(Froyen et al. 2008)

IL1RAPL1

300206

X-linked (MRX21)

Xp21.3–p21.2

Recessive

Truncating, deletion

(Carrie et al. 1999; Nawara et al. 2008)

JARID1C (KDM5C)

314690

X-linked

Xp11.22

Recessive

Truncating, missense

(Jensen et al. 2005)

KIRREL3

607761

Autosomal (MRD4)

11q24.2

Dominant

Missense

(Bhalla et al. 2008)

MAGT1

300715

X-linked (MRX95)

Xq21.1

Dominant

Missense

(Molinari et al. 2008)

MBD5

611472

Autosomal (MRD1)

2q23.1

Dominant

Deletion, missense

(Wagenstaller et al. 2007)

MECP2

300005

X-linked (MRXS13)

Xq28

Dominant

Truncating, missense, deletion

(Orrico et al. 2000)

NLGN4

300427

X-linked (AUTSX2)

Xp22.31–p22.32

Recessive

Truncating

(Laumonnier et al. 2004)

OPHN1

300127

X-linked

Xq12

Recessive

Truncating, deletion

(Billuart et al. 1998; Philip et al. 2003)

PAK3

300142

X-linked (MRX30)

Xq22.3

Recessive

Truncating, missense, splice site

(Allen et al. 1998; Rejab et al. 2008)

PQBP1

300463

X-linked

Xp11.23

Recessive

Missense

(Kalscheuer et al. 2003)

PRSS12

606709

Autosomal (MRT1)

4q26

Recessive

Truncating

(Molinari et al. 2002)

PTCHD1

 

X-linked

 

Recessive

Deletion

(Noor et al. in press)

RPS6KA3

300075

X-linked (MRX19)

Xp22.12

Recessive

Missense

(Merienne et al. 1999)

SHANK2

603290

Autosomal

11q13.3–13.4

Dominant

CNV deletion, missense

(Berkel et al. 2010)

SHROOM4

300579

X-linked

Xp11.22

Dominant

Translocation; missense

(Stocco dos Santos et al. 2003; Hagens et al. 2006)

SLC6A8

300036

X-linked

Xq28

Dominantb

Truncating, missense

(Salomons et al. 2001; Hahn et al. 2002)

STXBP1

602926

Autosomal

9q34.11

Dominant

Deletion, nonsense

(Hamdan et al. 2009a, b)

SYNGAP1

603384

Autosomal (MRD5)

6p21.32

Dominant

Truncating

(Hamdan et al. 2009a, b)

SYP

313475

X-linked

Xp11.23

Recessive

Truncating, missense

(Tarpey et al. 2009)

TSPAN7

300096

X-linked (MRX58)

Xp11.4

Recessive

Truncating, missense

(Zemni et al. 2000)

TRAPPC9

611966

Autosomal (MRT13)

8q24.3

Recessive

Truncating

(Mir et al. 2009

TUSC3

601385

Autosomal (MRT7)

8p22

Recessive

Truncating

(Garshasbi et al. 2008; Molinari et al. 2008)

UPF3B

300298

X-linked (MRXS14)

Xq24

Recessive

Truncating

(Tarpey et al. 2007)

ZNF41

314995

X-linked (MRX89)

Xp11.3

Variable

Missense, splice site

(Shoichet et al. 2003)

ZNF674

300573

X-linked (MRX92)

Xp11.3

Recessive

Truncating

(Lugtenberg et al. 2006

ZNF711

314990

X-linked

Xq21.1

Recessive

Truncating

(Tarpey et al. 2009)

ZNF81

314998

X-linked (MRX45)

Xp11.23

Recessive

Missense

(Kleefstra et al. 2004)

  1. *In X-linked genes, male and female values reflect the effects of one variant
  2. aCytoband reported in UCSC Genome Browser
  3. bless severe in females