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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