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Table 2 Rare variants found in CHH genes in 46,XY DSD patients

From: Variants in congenital hypogonadotrophic hypogonadism genes identified in an Indonesian cohort of 46,XY under-virilised boys

Patient ID

CHH gene

Variant location

Change

Variant details

dbSNP

EVS MAF

ExAC total freq.

ExAC SA/EA

ClinVar/HGMD

In silico predictions

GERP++ RS score

Previous functional studies

173

PROKR2

chr20:5283278-5283279

G/A

PROKR2:NM_144773:c.C563T:p.S188L

rs376239580

0.0077

0.00002

0/0

Yes—likely pathogenic for CHH

3 of 4

5.31

Cole et al. (2008); Zhu et al. (2015)

143

PROKR2

chr20:5283278-5283279

G/A

PROKR2:NM_144773:c.C563T:p.S188L

rs376239580

0.0077

0.00002

0/0

Yes—likely pathogenic for CHH

3 of 4

5.31

Cole et al. (2008); Zhu et al. (2015)

159

PROKR2

chr20:5282850-5282851

C/T

PROKR2:NM_144773:c.G991A:p.V331M

rs117106081

0.0154

0.00652

0.03119/0.02901

Yes—CHH

0 of 4

2.01

Dodé (2006); Monnier et al. (2009); Cole et al. (2008)

171

PROKR2

chr20:5282787-5282788

A/C

PROKR2:NM_144773:c.T1054G:p.W352G

Not found

0

0.00000

0.00

Not found

4 of 4

5.05

 

47

PROK2

chr3:71834136-71834137

C/T

PROK2:NM_001126128:c.G68A:p.R23H

Not found

0

0.00000

0/0

Not found

0 of 4

2.47

 

174

WDR11

chr10:122650293-122650294

G/T

WDR11:NM_018117:c.G2409T:p.W803C

Not found

0

0.00000

0/0

Not found

4 of 4

5.79

 

164

WDR11

chr10 :122630739-122630740

A/G

WDR11:NM_018117:c.A1352G:p.H451R

rs199920020

0

0.00007

0/0.00104

Not found

2 of 4

3.575

 

163

WDR11

chr10:122626666-122626667

T/A

WDR11:NM_018117:c.T1279A:p.L427I

Not found

0

0.00000

0/0

Not found

3 of 4

3.11

 

147

FGFR1

chr8:38287238-38287239

G/A

FGFR1:NM_001174063:c.C320T:p.S107L

rs140382957

0.0077

0.00253

0.0002393/0.0454

1 record—benign

2 of 4

3.6

Sato (2004); Sykiotis (2010); Fukami et al. (2013)

101

CHD7

chr8:61655556-61655557

G/T

CHD7: NM_017780:c.G1565T:p.G522V

rs142962579

0

0.00232

0.0003717/0.03098

Not found

3 of 4

5.67

 

FGFR1

chr8:38287238-38287239

G/A

FGFR1:NM_001174063:c.C320T:p.S107L

rs140382957

0.0077

0.00253

0.0002393/0.0454

1 record—benign

2 of 4

3.6

Sato (2004), Sykiotis (2010); Fukami et al (2013)

169

FGFR1

chr8:38287238-38287239

G/A

FGFR1:NM_001174063:c.C320T:p.S107L

rs140382957

0.0077

0.00253

0.0002393/0.0454

1 record—benign

2 of 4

3.6

Sato (2004); Sykiotis (2010); Fukami et al. (2013)

CHD7

chr8:61713055-61713056

C/T

CHD7:NM_017780:c.C2347T:p.P783S

rs373873996

0

0.00009

6.152e−05/0.00117

1 record—benign for CHARGE

2 of 4

5.81

 

LEP

chr7:127892124-127892125

A/G

LEP:NM_000230:c.A53G:p.Y18C

rs148407750

0.0461

0.00041

6.056e−05/0.003004

Not found

0 of 4

1.13

 
  1. Patient number is shown and the gene, variant location and DNA change. The allele frequency (from ExAC) is shown for all populations (MAF) and also specifically for both South Asia (AS) and East Asia (EA). Details are shown in the variant in found in Clinvar or in HMGD, and if reported previously, the reference is shown. Four in silico prediction programs were used for each variant, and the number of these showing a likely pathogenic/damaging score is shown. GERP++ scores are also shown