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. Author manuscript; available in PMC: 2014 Jun 11.
Published in final edited form as: Clin Genet. 2012 May 1;83(1):35–43. doi: 10.1111/j.1399-0004.2012.01879.x

Table 2.

Filtered SNVs and INDELs identified in DSD patientsa

Sample Chr Start End Gene SNV
INDEL		 SNP
quality		 Protein change Causative
variant?		 In HGMD
public?		 In
dbSNP132
(1 %)?		 Polyphen-2 sift Mutation
Assessor
47, XXY KS chr10 104586872 104586873 CYP17A1 T→G 34 H79P – N N Possibly
 damaging		 Tolerated Low
47, XXY KS chr8 106870217 106870218 ZFPM2 G→C 114 S210T – N N Benign Tolerated Neutral
DSDPtl chr2 31607980 31607981 SRD5A2 C→T 225 E200K Y Y N – – Medium
DSDPt3 chr8 11651992 11651993 GATA4 G→A 228 V380M – N rs114868912 Benign Tolerated Neutral
DSDPt3 chr9 1046731 1046732 DMRT2 G→A 194 R382Q – N rs72703237 Benign Tolerated Neutral
DSDPt3 chr17 75373191 75373192 CBX2 C→T 228 A452V – N rs76915888 Benign Tolerated Neutral
DSDPt3 chr9 1046397 1046398 DMRT2 C→G 100 P271A – N rs72703236 Probably
 damaging		 Damaging Medium
DSDPt3 chrY 2715264 2715265 SRY T→C 225 Y127C Y Y N Probably
 damaging		 – –
DSDPt5 chr12 52104848 52104849 AMHR2 A→C 136 T108P – N N Possibly
 damaging		 Tolerated Neutral
DSDPt5 chr8 106870217 106870218 ZFPM2 G→C 228 S210T – N N Benign Tolerated Neutral
DSDPt6 chr17 75373191 75373192 CBX2 C→T 228 A452V – N rs76915888 Benign Tolerated Neutral
DSDPt6 chrX 139414764 139414765 S0X3 C→T 228 A43T – N N Benign – Neutral
DSDPt7 chrX 66858443 66858444 AR T→C 225 M788T Y Y N Probably
 damaging		 Damaging Medium
DSDPt8 chrX 30237128 30237129 NR0B1 G→T 212 Y121 * Y Y N Termination Termination Termination
DSDPt9 chr9 884196 884197 DMRT1 T→G 46 V→Gb – N rs116766038 Non-coding
 by CCDS		 Non-coding
 by CCDS		 Non-coding
 by CCDS
DSDPt9 chr15 72424436 72424437 CYP11A1 INS:→A 208 Intronic splice-site
 mutation		 Y N N INDELc INDEL INDEL
DSDPt9 chr15 72422525 72422526 CYP11A1 DEL:T→- 726 Frameshift,
 early-termination		 Y Y N INDEL INDEL INDEL
DSDPtl 1 chr15 72446744 72446745 CYP11A1 C→T 204 V79I – N N Benign Tolerated Low
DSDPtl 2 chrX 76824270 76824271 ATRX T→C 139 K1045E Y N N Probably
 damaging		 Tolerated Low

CCDS, consensus coding sequence; DSD, disorders of sex development; HGMD, Human Gene Mutation Database; INDELs, insertions and deletions; N, no; SNV, single-nucleotide variant; Y, yes.

a

High-quality SNVs with coding consequences identified in the 16 patients were run through a series of filters such as HGMD to identify SNVs and INDELs previously reported in the literature. All INDELs were reported as causative. Remaining SNVs were filtered using dbSNP132 (≥1% frequency) to identify rare variants. The identified rare SNV variants were then run through multiple in silico protein pathogenicity predictors to determining whether the coding variation was likely to be causative of the disease. Two of three pathogenicity predictors were required to indicate the mutation was ‘damaging’ in order for it to be classified as causative.

b

This mutation lies in the coding region of an isoform of DMRT1.

c

In silico protein predictors do not provide pathogenicity for INDELs.