Table 2.
Top 15 allele frequencies of pathogenic variants identified in the Southern Chinese populations.
| 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 |
aCarrier rate was calculated from genome sequencing samples (n = 427) but not exome sequencing samples.
Southeast Asian deletion (--SEA) and rightward deletion (-α3.7) are the top two deletions responsible for α-thalassaemia.