{{Rsnum
|rsid=1132200
|Gene=TMEM39A
|Chromosome=3
|position=119431989
|Orientation=minus
|GMAF=0.08678
|Assembly=GRCh38
|GenomeBuild=38.1
|dbSNPBuild=141
|geno1=(A;A)
|geno2=(A;G)
|geno3=(G;G)
|Gene_s=TMEM39A
}}{{ population diversity
| geno1=(A;A)
| geno2=(A;G)
| geno3=(G;G)
| CEU | 0.9 | 23.0 | 76.1
| HCB | 0.7 | 15.3 | 83.9
| JPT | 0.0 | 15.0 | 85.0
| YRI | 0.0 | 0.0 | 100.0
| ASW | 0.0 | 7.0 | 93.0
| CHB | 0.7 | 15.3 | 83.9
| CHD | 0.0 | 19.3 | 80.7
| GIH | 4.0 | 27.7 | 68.3
| LWK | 0.0 | 2.8 | 97.2
| MEX | 0.0 | 6.9 | 93.1
| MKK | 0.0 | 9.6 | 90.4
| TSI | 2.9 | 34.3 | 62.7
| HapMapRevision=28
}}{{PMID Auto
|PMID=20007504
|Title=Comprehensive follow-up of the first genome-wide association study of multiple sclerosis identifies KIF21B and TMEM39A as susceptibility loci
|OA=1
}}

{{PMID Auto
|PMID=22464253
|Title=Identification of IRF8, TMEM39A, and IKZF3-ZPBP2 as susceptibility loci for systemic lupus erythematosus in a large-scale multiracial replication study
|OA=1
}}

{{PMID Auto
|PMID=20041220
|Title=Autoimmune disease classification by inverse association with SNP alleles.
|OA=1
}}

{{PMID Auto
|PMID=20405052
|Title=The effect of single nucleotide polymorphisms from genome wide association studies in multiple sclerosis on gene expression.
|OA=1
}}

{{GET Evidence
|gene=TMEM39A
|aa_change=Ala487Thr
|aa_change_short=A487T
|impact=not reviewed
|qualified_impact=Insufficiently evaluated not reviewed
|inheritance=unknown
|quality_scores=Array
|dbsnp_id=rs1132200
|overall_frequency_n=1251
|overall_frequency_d=10756
|overall_frequency=0.116307
|n_genomes=5
|n_genomes_annotated=0
|n_haplomes=5
|n_articles=0
|n_articles_annotated=0
|pph2_score=0.035
|nblosum100=1
|autoscore=0
|webscore=N
}}

{{PMID Auto
|PMID=22194214
|Title=Replication study of 10 genes showing evidence for association with multiple sclerosis: validation of TMEM39A, IL12B and CBLB [correction of CLBL] genes
}}

{{on chip | 23andMe v1}}
{{on chip | 23andMe v2}}
{{on chip | 23andMe v3}}
{{on chip | 23andMe v4}}
{{on chip | Affy GenomeWide 6}}
{{on chip | FTDNA2}}
{{on chip | FTDNA}}
{{on chip | HumanOmni1Quad}}
{{on chip | Illumina Human 1M}}