Table 2 Top 15 allele frequencies of pathogenic variants identified in the Southern Chinese populations.

From: Comprehensive analysis of recessive carrier status using exome and genome sequencing data in 1543 Southern Chinese

Gene

Condition

mRNA accession

Mutation Type

Nucleotide change

Protein change

dbsnp ID

Rate % (no. of samples)

Allele Frequency

gnomAD_EAS

GJB2

Deafness, Autosomal Recessive 1A; DFNB1A

NM_004004.6

Missense

c.109G>A

p.(Val37Ile)

rs72474224

22.49 (347)

0.11990

0.08345

HBA1/HBA2

Thalassaemia, Alpha-

 

–SEA

   

4.45 (19)a

0.02225a

 

HBA1/HBA2

Thalassaemia, Alpha-

 

-α3.7

   

3.04 (13)a

0.01522a

 

SMN1

Spinal Muscular Atrophy, Type I

 

SMN1 exon 7 deletion

   

1.64 (7)a

0.0082a

 

GALC

Krabbe Disease

NM_000153.4

Missense

c.1901T>C

p.(Leu634Ser)

rs138577661

1.43 (22)

0.00713

0.00830

GJB2

Deafness, Autosomal Recessive 1A; DFNB1A

NM_004004.6

Frameshift

c.235delC

p.(Leu79CysfsTer3)

rs80338943

1.36 (21)

0.00680

0.00652

SLC25A13

Citrullinemia Type II, Neonatal-onset

NM_001160210.1

Frameshift

c.852_855delTATG

p.(Met285ProfsTer2)

rs80338720

1.36 (21)

0.00680

0.00461

SLC26A4

Pendred Syndrome

NM_000441.2

Splice

c.919-2A>G

p.?

rs111033313

1.30 (20)

0.00648

0.00506

POLG

POLG-Related Disorders

NM_001126131.2

Missense

c.2890C>T

p.(Arg964Cys)

rs201477273

1.23 (19)

0.00616

0.00902

HBB

Hb Beta Chain-Related Haemoglobinopathy (including Beta Thalassaemia and Sickle Cell Disease)

NM_000518.5

Frameshift

c.126_129delCTTT

p.(Phe42LeufsTer19)

rs80356821

0.97 (15)

0.00486

0.00231

SLC22A5

Carnitine Deficiency, Systemic primary

NM_003060.4

Missense

c.1400C>G

p.(Ser467Cys)

rs60376624

0.91 (14)

0.00454

0.00226

SLC25A20

Carnitine-acylcarnitine translocase deficiency

NM_000387.6

Splice

c.199-10T>G

p.?

rs541208710

0.78 (12)

0.00389

0.00095

SMN1

Spinal Muscular Atrophy, Type I

 

SMN1 silent mutation

   

0.47 (2)a

0.00234a

 

G6PC

Glycogen Storage Disease, Type Ia

NM_000151.4

Synonymous

c.648G>T

p.(Leu216 = )

rs80356484

0.45 (7)

0.00227

0.00110

PAH

Phenylketonuria

NM_000277.3

Missense

c.721C>T

p.(Arg241Cys)

rs76687508

0.39 (6)

0.00194

0.00146

ATP7B

Wilson Disease

NM_000053.4

Missense

c.2975C>T

p.(Pro992Leu)

rs201038679

0.39 (6)

0.00194

0.00046

SLC22A5

Carnitine Deficiency, Systemic primary

NM_003060.4

Missense

c.51C>G

p.(Phe17Leu)

rs11568520

0.39 (6)

0.00194

0.00166

SLC22A5

Carnitine Deficiency, Systemic primary

NM_003060.4

Nonsense

c.760C>T

p.(Arg254Ter)

rs121908893

0.39 (6)

0.00194

0.00145

  1. aCarrier rate was calculated from genome sequencing samples (n = 427) but not exome sequencing samples.
  2. Southeast Asian deletion (--SEA) and rightward deletion (-α3.7) are the top two deletions responsible for α-thalassaemia.
Back to article page