Table 1 CX3CR1 variants identified in this study

From: Rare genetic variants in CX3CR1 and their contribution to the increased risk of schizophrenia and autism spectrum disorders

Chr

Position (dbSNPID)

Transcript variant

Amino acid variant

SCZ (n=370)

ASD (n=192)

Our cohort a

MAF

HGVD a

MAF

iJGVD a

MAF

ExAC (Asian) a

MAF

ExAC (all) a

MAF

1000 Genomes a

MAF

In silico analysis

            

PolyPhen-2

MutationTaster

3

39266096

(rs758302878)

c.414G>T

Met138Ile

1F

—

1/1122

8.9 × 10−4

—

—

6/8626

7 × 10−4

6/120 720

5 × 10−5

—

Benign

Disease causing

3

39266175

(rs201442030)

c.335G>C

Gly112Ala

1F, 1M

2M

4/1112

3.6 × 10−3

2/1102

1.8 × 10−3

6/4084

1.5 × 10−3

28/8624

3.2 × 10−3

36/120 712

3 × 10−4

1/1008

1 × 10−3

Probably

Damaging

Polymorphism

3

39266347

(rs750585901)

c.163G>A

Ala55Thr

1M

1M

2/1122

3.6 × 10−3

—

1/4076

2.5 × 10−4

1/8626

1.2 × 10−4

1/120 768

8.3 × 10−6

—

Benign

Disease causing

  1. Abbreviations: 1000 Genomes, the 1000 Genomes Project (http://www.1000genomes.org); ASD, autism spectrum disorders; Chr, chromosome; dbSNP, dbSNP build 149 (http://www.ncbi.nlm.nih.gov/projects/SNP/); ExAC, Exome Aggregation Consortium (http://exac.broadinstitute.org); F, female; HGVD, the Human Genetic Variation Database (http://www.genome.med.kyoto-u.ac.jp/SnpDB/); iJGVD, the integrative Japanese Genome Variation Database (https://ijgvd.megabank.tohoku.ac.jp); M, male; MAF, minor allele frequency; SCZ, schizophrenia.
  2. aMinor allele count/total allele count.
  3. Note: Genomic position based on NCBI builds GRCh38 (Ensembl Transcript ID ENST000000399220). Amino acid position is based on NCBI reference sequence NP_001328.1.
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