Table S3: Top 10 list of the population sampling probability (PSAP) results. The two variants in the stromal antigen 3 (STAG3) gene are highlighted
VAN DER BIJL, N., et al. Mutations in the stromal antigen 3 (STAG3) gene cause male infertility due to meiotic arrest. Human Reproduction, 2019, 34. Jg., Nr. 11, S. 2112-2119.
Publication: https://doi.org/10.1093/humrep/dez204
Description
Chr: Chromosome, Start: Genomic position, Ref: Reference allele, Gene.wgEncodeGencodeBasicV19: Gene name (GENCODE Release 19), Func.wgEncodeGencodeBasicV19: Regions (e.g. exonic, intronic) affected by variant (GENCODE Release 19), ExonicFunc.wgEncodeGencodeBasicV19: Exonic consequence (e.g. stopgain, frameshift insertion) of variant (GENCODE Release 19), AAChange.wgEncodeGencodeBasicV19: Amino acid changes caused by variant (GENCODE Release 19), mac63kFreq_ALL: Variant allele frequency in Exome Aggregation Consortium (ExAC) 0.2 database, 1000g2014sep_all: Variant allele frequency in 1000 Genomes Project phase 3 database, esp6500si_all: Variant allele frequency in NHLBI Exome Sequencing Project 6500 (ESP6500) database, Alt: Alternative allele, CADD_Phred: Variant combined annotation-dependent depletion (CADD) score, Geno: Genotype (hom = homozygous, het = heterozygous), Dz.Model: Disease model assumed
Disclaimer
The publication Mutations in the stromal antigen 3 (STAG3) gene cause male infertility due to meiotic arrest. by Nils van der Bijl, Albrecht Röpke, Uddipta Biswas, Marius Wöste, Rolf Jessberger, Sabine Kliesch, Corinna Friedrich, Frank Tüttelmann is published under an open access license: http://creativecommons.org/licenses/by-nc/4.0/. Permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited.
Curation by the MFGA team
Pie chart of selected column
Table
CHR | GENE | STARTPOSITION | Ref | Func.wgEncodeGencodeBasicV19 | ExonicFunc.wgEncodeGencodeBasicV19 | AAChange.wgEncodeGencodeBasicV19 | Alt | Geno | Dz.model | TestisExpression | Mac63kFreq_All | 1000g2014sep_all | Esp6500si_all | Cadd_phred | Popscore |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
12 | HNF1A | 121434630 | - | exonic;intronic | frameshift insertion | HNF1A:ENST00000543427.1:exon7:c.1043_1044insTCATTCAT:p.T348fs;HNF1A:ENST00000402929.1:exon6:c.1394_1395insTCATTCAT:p.T465fs | TCATTCAT | hom | REC-hom | faintly | 29.6 | 1.00000000002876E-06 | |||
7 | STAG3 | 99796115 | T | exonic | nonsynonymous SNV | STAG3:ENST00000317296.5:exon13:c.T1262G:p.L421R;STAG3:ENST00000426455.1:exon13:c.T1262G:p.L421R;STAG3:ENST00000394018.2:exon11:c.T1088G:p.L363R | G | het | REC-chet | highly | 21 | 1.99999999994649E-06 | |||
1 | CDCP2 | 54605318 | - | exonic | frameshift insertion | CDCP2:ENST00000371330.1:exon4:c.1224dupC:p.M409fs | G | hom | REC-hom | faintly | 43 | 2.99999999997524E-06 | |||
5 | NOP16 | 175811094 | - | exonic;UTR3;downstream | frameshift insertion | NOP16:ENST00000510123.1:exon5:c.583_584insAC:p.R195fs | GT | hom | REC-hom | ubiquitous | 23.4 | 2.99999999997524E-06 | |||
12 | WNK1 | 974308 | - | exonic;intronic | frameshift insertion | WNK1:ENST00000530271.2:exon9:c.2173dupC:p.V724fs | C | hom | REC-hom | ubiquitous | 45 | 5.00000000003276E-06 | |||
X | GRIA3 | 122336600 | - | exonic;intronic | frameshift insertion | GRIA3:ENST00000371266.1:exon4:c.382dupG:p.G127fs;GRIA3:ENST00000371264.3:exon3:c.382dupG:p.G127fs | G | hom | REC-hom | faintly | 37 | 1.49999999999872E-05 | |||
16 | HYDIN | 70896016 | A | exonic | frameshift deletion | HYDIN:ENST00000393567.2:exon69:c.11712delT:p.I3904fs | - | het | DOM-het | highest | 48 | 9.80000000000425E-05 | |||
7 | STAG3 | 99796165 | C | exonic | stopgain | STAG3:ENST00000317296.5:exon13:c.C1312T:p.R438X;STAG3:ENST00000426455.1:exon13:c.C1312T:p.R438X;STAG3:ENST00000394018.2:exon11:c.C1138T:p.R380X | T | het | DOM-het | highly | 3.253E-05 | 36 | 0.000369 | ||
17 | DUS1L | 80022791 | G | exonic | nonsynonymous SNV | DUS1L:ENST00000306796.5:exon2:c.C145G:p.L49V;DUS1L:ENST00000354321.7:exon1:c.C145G:p.L49V | C | het | DOM-het | ubiquitous | 21.7 | 0.000731 | |||
19 | LTBP4 | 41114171 | C | exonic;UTR5 | nonsynonymous SNV | LTBP4:ENST00000396819.3:exon8:c.C1202T:p.S401L;LTBP4:ENST00000204005.9:exon11:c.C1292T:p.S431L;LTBP4:ENST00000308370.7:exon11:c.C1403T:p.S468L | T | het | DOM-het | ubiquitous | 8.166E-06 | 8.2E-05 | 32 | 0.00109 |