Male Fertility Gene Atlas

CRU Male Germ Cells

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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