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Table 3 Gene mutations found in 61 Chinese patients with PA

From: Prevalence of propionic acidemia in China

Number

Exon/Intron

Nucleotide alteration

Protein alteration

Mutation type

Early/late onset

ACMG classification

CADD scores

MSC scores

References

Clinical features

Treatment

Outcome

PCCA

1

Exon10

NM_000282.4:c.802C > T

p.Arg268Cys

Missense

Late

Pathogenic

22.5

20

[110]

No specific clinical symptoms

NA

Following up eleven times within one year and three months after birth, liver and kidney function were normal

 

Exon11

NM_000282.4:c.827delG

p.Gly276Valfs*46

Frameshift

Likely Pathogenic

NA

NA

2

Intron8

NM_000282.4:c.638-1G > C

NA

Splice site mutation

Early

Likely Pathogenic

33

20

[61]

Mild anemia or mild jaundice, hyperammonemia, hyperlactatemia and hypoglycemia

Protein restriction with special protein powder and sufficient calories, L-carnitine and arginine supplementation, and regular follow-up checks

Normal development and no acute metabolic disorders were observed during the course of management

 

NA

NA

NA

NA

NA

NA

NA

3

Exon9

NM_000282.4:c.688C > T

p.Arg230Cys

Missense

Pathogenic

28.3

20

 

Intron13

NM_000282.4:c.1209 + 2 T > G

NA

Splice donor

Pathogenic

34

20

4

Intron2

NM_000282.4:c.183 + 1G > C

NA

Splice site mutation

Likely Pathogenic

33

20

 

Exon21

NM_000282.4:c.1850 T > C

p.Leu617Pro

Missense

Likely Benign

24.5

20

5

Exon22

NM_000282.4:c.2002G > A

p.Gly668Arg

Missense

Pathogenic

32

20

Development delay in early infancy

 

Exon22

NM_000282.4:c.2040G > A

p.Ala680Ala

Synonymous

Likely Pathogenic

24

20

6

Exon22

NM_000282.4:c.2002G > A

p.Gly668Arg

Missense

Pathogenic

32

20

 

Exon2

NM_000282.4:c.131delinsATT

p.Cys44Tyrfs*3

Missense

Pathogenic

NA

NA

7

Intron3

NM_000282.4:c.231 + 1G > A

NA

Splice site mutation

Likely Pathogenic

34

20

NA

 

Exon7

NM_000282.4:c.596 T > A

p.Val199Asp

Missense

Uncertain Significance

28.1

20

8

Exon22

NM_000282.4:c.2002G > A

p.Gly668Arg

Missense

Early

Pathogenic

32

20

[59]

Respiratory failure, granulocytopenia, and cardiac damage with rapid progression

Anti-infection measures, atomization therapy, sputum suction, glucose infusion, protein restriction, and supplementation with calcium, arginine, l-carnitine, and l-creatinine phosphate. Efforts were also made to strengthen the respiratory tract and correct acidosis

Died at the age of eighth day after birth

 

Exon22

NM_000282.4:c.2002G > A

p.Gly668Arg

Missense

Pathogenic

32

20

9

Exon22

NM_000282.4:c.2002G > A

p.Gly668Arg

Missense

Pathogenic

32

20

Disorders of consciousness, poor feeding, hyperammonemia, and metabolic acidosis

Anti-infection, fasting, restriction of protein intake, supplementation of hypertonic glucose, arginine iv to promote ammonia excretion

Died at the age of one month and seven days after birth

 

Exon22

NM_000282.4:c.2002G > A

p.Gly668Arg

Missense

Pathogenic

32

20

10

Intron20

NM_000282.4:c.1845 + 1G > A

NA

Splice site mutation

Early

Pathogenic

34

20

[111]

NA

NA

Died during the neonatal period

 

Exon6

NM_000282.4:c.446del

p.Asn149Thrfs*35

Frameshift

Pathogenic

NA

NA

11

Intron20

NM_000282.4:c.1845 + 1G > A

NA

Splice site mutation

NA

Pathogenic

34

20

Coma, convulsions, bronchopneumonia, anemia, thrombocytopenia

NA

Died after more than seven months old

 

Exon6

NM_000282.4:c.446del

p.Asn149Thrfs*35

Frameshift

Pathogenic

NA

NA

12

Exon3

NM_000282.4:c.229C > T

p.Arg77Trp

Missense

NA

Pathogenic

25.1

20

[112]

NA

NA

NA

 

Intron21

NM_000282.4:c.1899 + 1G > A

NA

Splice site mutation

Likely Pathogenic

NA

NA

13

Exon14

NM_000282.4:c.1262A > C

p.Gln421Pro

Missense

Newborn screening

Uncertain Significance

22.8

20

[64]

No typical PA symptoms, no hyperammonemia

Low-protein diet and l-carnitine supplementation

No significant development delay

 

Exon3

NM_000282.4:c.229C > T

p.Arg77Trp

Missense

Pathogenic

25.1

20

14

Exon15

NM_000282.4:c.1288C > T

p.Arg430Ter

Nonsense

Newborn screening

Pathogenic

37

20

[113]

NA

NA

NA

 

Exon3

NM_000282.4:c.229C > T

p.Arg77Trp

Missense

Pathogenic

25.1

20

15

Intron13

NM_000282.4:c.1210-7C > G

NA

Splice site mutation

Newborn screening

Uncertain Significance

25.3

20

NA

NA

NA

 

Exon13

NM_000282.4:c.1185A > C

p.Ala395Ala

Samesense

Likely Benign

9.037

20

16

Exon22

NM_000282.4:c.2002G > A

p.Gly668Arg

Missense

Newborn screening

Pathogenic

32

20

[114]

NA

NA

NA

 

Exon22

NM_000282.4:c.2002G > A

p.Gly668Arg

Missense

Pathogenic

32

20

17

Exon12

NM_000282.4:c.937C > T

p.Arg313Ter

Nonsense

Early

Pathogenic

38

20

[37]

Tachypnea, poor reaction, seizures, lethargy, irritability

Antibiotics treatment, supplementation of l-carnitine, folic acid, and biotin; protein restriction

Died at approximately two months of age

 

Exon10-

NM_000282.4:c.773_819 + 47delinsAA

NA

Complex deletion–

Likely Pathogenic

NA

NA

Intron10

Insertion (delins) mutation

18

Exon15

NM_000282.4:c.1288C > T

p.Arg430Ter

Nonsense

Early

Pathogenic

37

20

[7]

Generalized tonic–clonic seizures, metabolic acidosis and hyperammonemia

NA

Died at six and a half months old from sudden cardiac arrest

 

Exon22

NM_000282.4:c.2002G > A

p.Gly668Arg

Missense

Pathogenic

32

20

19

Exon16

NM_000282.4:c.1426C > T

p.Arg476Ter

Nonsense

Early

Pathogenic

41

20

Recurrent vomiting, lethargy and dyspnea

Low-isoleucine, − methionine, − threonine,

and-valine diet, supplementation of l-carnitine and biotin

Mild intellectual disability

 

Exon16

NM_000282.4:c.1426C > T

p.Arg476Ter

Nonsense

Pathogenic

41

20

20

Exon19

NM_000282.4:c.1746G > C

P.Ser582Ser

Synonymous

Early

Uncertain Significance

9.081

20

[36]

Cough, tachypnea, dyspnea and metabolic acidosis

NA

Died due to respiratory failure

 

Exon3-4

NM_000282.4:Exon3-4del

NA

NA

NA

NA

NA

21

Exon19

NM_000282.4:c.1746G > C

P.Ser582Ser

Synonymous

Early

Uncertain Significance

9.081

20

Cough, tachypnea, dyspnea and metabolic acidosis

NA

NA

 

Exon3-4

NM_000282.4:Exon3-4del

NA

NA

NA

NA

NA

22

Exon22

NM_000282.4:c.2002G > A

p.Gly668Arg

Missense

Late

Pathogenic

32

20

[62]

Poor feeding, intermittent vomiting, dilated cardiomyopathy

Liver transplantation

Liver transplantation improved cardiac function but did not significantly impact growth, even with a normal diet, except when supplemented with l-carnitine

 

Exon22

NM_000282.4:c.2002G > A

p.Gly668Arg

Missense

Pathogenic

32

20

23

Exon21

NM_000282.4:c.1850 T > C

p.Leu617Pro

Missense

Newborn screening

Likely Benign

24.5

20

[108]

NA

NA

NA

 

Exon4

NM_000282.4:c.297 T > A

p.Ser99Arg

Missense

Uncertain Significance

20.4

20

24

Intron15

NM_000282.4:c.1353 + 5_1353 + 9del

NA

Splice site mutation

Late

Uncertain Significance

NA

NA

[52]

NA

Low protein diet, special milk powder, oral l-carnitine and arginine

Physical and intellectual development is normal and noacute metabolic disorders

 

NA

NA

NA

NA

NA

NA

NA

25

Exon3

NM_000282.4:c.229C > T

p.Arg77Trp

Missense

Newborn screening

Pathogenic

25.1

20

[109]

NA

NA

NA

 

Exon22

NM_000282.4:c.2002G > A

p.Gly668Arg

Missense

Pathogenic

32

20

PCCB

1

Exon13

NM_000532.5:c.1301C > T

p.Ala434Val

Missense

Early

Pathogenic

32

20

[65]

Poor feeding, hyperglycinemia, hyperammonemia, metabolic acidosis, early recurrent infections, and development delay

Sodium bicarbonate IV to correct acidosis, l-carnitine supplementation, BCAA restriction and protein intake reduction

Obvious development delay and intellectual disability

 

Exon13

NM_000532.5:c.1301C > T

p.Ala434Val

Missense

Pathogenic

32

20

2

Exon1

NM_000532.5:c.167_179del13insC

p.Asp56_Lys60delinsAla

Deletion and insertion mutation

Late

NA

NA

NA

Hyperglycininemia

l-carnitine supplementation, BCAA restriction and protein intake reduction

Mental and language development is slightly delayed

 

Exon1

NM_000532.5:c.167_179del13insC

p.Asp56_Lys60delinsAla

Deletion and insertion mutation

NA

NA

NA

3

Exon1

NM_000532.5:c.132_134delGACinsAT

p.Thr45SerfsTer20

Deletion and insertion mutation

Early

Likely Pathogenic

NA

NA

[115]

Repeated seizures, hyperammonemia, ketoacidosis, hyperglycaemia, anemia

Protein restriction along with phenobarbital, l-carnitine, and arginine supplementation. Treatments to correct acidosis and electrolyte disorders

Symptoms were improved

 

NA

NA

NA

NA

NA

NA

NA

4

Exon14

NM_000532.5:c.1403C > T

p.Ala468Val

Missense

Early

Likely Pathogenic

27.1

20

[61]

Mild anemia or mild jaundice, metabolic acidosis, hyperammonemia, hyperlactatemia and hypoglycemia

Similar to PCCA cases No. 2- 7

Physical and intellectual development is normal

 

Exon8

NM_000532.5:c.838dup

p.Leu280fs

Frameshift

Pathogenic

NA

NA

5

Intron1

NM_000532.5:c.184-2A > G

NA

Splice site mutation

Early

Pathogenic

33

20

Repeated vomiting, lethargy, dyspnea, hypotonia, metabolic acidosis, hyperammonemia, liver dysfunction

Death from an acute metabolic disorder occurred at the age of seven months

 

Exon7

NM_000532.5:c.733G > A

p.Gly245Ser

Missense

Likely Pathogenic

28.9

20

6

Exon3

NM_000532.5:c.331C > T

p.Arg111Ter

Nonsense

Early

Pathogenic

36

20

[116]

Lethargy, poor feeding

l-carnitine, special milk powder

Died at three months old after birth

 

Exon12

NM_000532.5:c.1228C > T

p.Arg410Trp

Missense

Pathogenic

37

20

7

Exon1

NM_000532.5:c.146delG

p.Gly49Glufs*16

Frameshift

Late

Likely Pathogenic

NA

NA

Vomiting, lethargy, poor spirit

l-carnitine, special milk powder

Poor compliance and intermittent treatment, significant development delay

 

Exon12

NM_000532.5:c.1253C > T

p.Ala418Val

Missense

Likely Pathogenic

27.4

20

8

Exon10

NM_000532.5:c.1087 T > C

p.Ser363Pro

Missense

Late

Likely Pathogenic

30

20

[47]

NA

NA

NA

 

Exon10

NM_000532.5:c.1087 T > C

p.Ser363Pro

Missense

Likely Pathogenic

30

20

9

Intron1

NM_000532.5:c.184-2A > G

NA

Splice site mutation

Early

Pathogenic

33

20

[117]

Abdominal distension, vomiting, poor feeding, dyspnea, and hyperammonemia

NA

NA

 

Exon7

NM_000532.5:c.733G > A

p.Gly245Ser

Missense

Likely Pathogenic

28.9

20

10

NA

NA

NA

NA

Late

NA

NA

NA

[64]

Recurrent vomiting, disorders of consciousness, hyperventilation, and metabolic acidosis

NA

Died at the age of two years and eight months after birth

 

NA

NA

NA

NA

NA

NA

NA

11

Exon13

NM_000532.5:c.1316A > G

p.Tyr439Cys

Missense

Prenatal diagnosis

Pathogenic

31

20

NA

NA

Miscarriage occurred at twenty-one weeks of gestation

 

Intron1

NM_000532.5:c.-4156_183 + 3713del

NA

NA

NA

NA

NA

12

Exon13

NM_000532.5:c.1301C > T

p.Ala434Val

Missense

Early

Pathogenic

32

20

Jaundice, poor feeding, hypotonia, metabolic acidosis, hyperglycaemia, and hyperammonemia

NA

NA

 

Exon5

NM_000532.5:c.580 T > C

p.Ser194Pro

Missense

Likely Pathogenic

28.8

20

13

Exon13

NM_000532.5:c.1301C > T

p.Ala434Val

Missense

Early

Pathogenic

32

20

Poor feeding, severe jaundice, metabolic acidosis, and hyperammonemia

NA

Died at the age of one year and eight months after birth

 

Exon13

NM_000532.5:c.1301C > T

p.Ala434Val

Missense

Pathogenic

32

20

14

NA

NA

NA

NA

Early

NA

NA

NA

Poor feeding, vomiting, hyperammonemia, metabolic acidosis, and recurrent infections

NA

Died at the age of one year and six months of a severe infection

 

NA

NA

NA

NA

NA

NA

NA

15

Intron1

NM_000532.5:c.-4156_183 + 3713del

NA

NA

Prenatal diagnosis

NA

NA

NA

Poor feeding, vomiting, and hyperammonemia

l-carnitine, special milk powder, phenylbutyric acids

Moderate developmental delay

 

Exon13

NM_000532.5:c.1301C > T

p.Ala434Val

Missense

Pathogenic

32

20

16

Exon13

NM_000532.5:c.1301C > T

p.Ala434Val

Missense

Newborn screening

Pathogenic

32

20

Classic PA phenotype and moderate developmental delay

Low-protein diet supplemented with l-carnitine, metronidazole, and growth

hormone, liver transplantation

No classical PA phenotypic symptoms was observed during the twelve-month follow-up after liver transplantation

 

Exon15

NM_000532.5:c.1534C > T

p.Arg512Cys

Missense

Pathogenic

28.6

20

17

Exon13

NM_000532.5:c.1301C > T

p.Ala434Val

Missense

Early

Pathogenic

32

20

Hypoactivity, poor feeding and tachypnea

hypotonia, hepatomegaly, disorders of consciousness, and hyperammonemia

NA

Died at six days old after birth

 

Exon8

NM_000532.5:c.838dup

p.Leu280fs

Frameshift

Pathogenic

NA

NA

18

Intron1

NM_000532.5:c.-4156_183 + 3713del

NA

NA

Newborn screening

NA

NA

NA

Hyperammonemia and hypoglycemia

Low-protein diet supplemented with l-carnitine

Mild development delay

 

Exon13

NM_000532.5:c.1301C > T

p.Ala434Val

Missense

Pathogenic

32

20

19

Exon8

NM_000532.5:c.838dup

p.Leu280fs

Frameshift

Newborn screening

Pathogenic

NA

NA

[67]

NA

NA

NA

 

Exon13

NM_000532.5:c.1316A > G

p.Tyr439Cys

Missense

Pathogenic

31

20

20

Exon8

NM_000532.5:c.838dup

p.Leu280fs

Frameshift

Pathogenic

NA

NA

 

Exon13

NM_000532.5:c.1316A > G

p.Tyr439Cys

Missense

Pathogenic

31

20

21

Exon3

NM_000532.5:c.370C > T

p.Gln124Ter

Nonsense

Likely Pathogenic

48

20

 

Exon12

NM_000532.5:c.1283C > T

p.Thr428Ile

Missense

Pathogenic

27.9

20

22

Exon3

NM_000532.5:c.331C > T

p.Arg111Ter

Nonsense

Pathogenic

36

20

 

Exon10

NM_000532.5:c.1087 T > C

p.Ser363Pro

Missense

Likely Pathogenic

30

20

23

Exon12

NM_000532.5:c.1220del

p.Gly407Alafs*36

Frameshift

Pathogenic

NA

NA

 

Exon10

NM_000532.5:c.1015A > T

p.Asn339Asp

Missense

Likely Pathogenic

29.3

20

24

Exon13

NM_000532.5:c.1316A > G

p.Tyr439Cys

Missense

Newborn screening

Pathogenic

31

20

 

NA

NA

NA

NA

NA

NA

NA

25

Exon8

NM_000532.5:c.838dup

p.Leu280fs

Frameshift

Early

Pathogenic

NA

NA

[16]

Hypotonia, disorders of consciousness, pancytopenia metabolic acidosis and hyperammonemia

Protein restriction and supplementation of l-carnitine, mannitol, and calories. Correct acidosis and electrolyte disorders

Died from pneumonia approximately thirty days after birth

 

Exon8

NM_000532.5:c.838dup

p.Leu280fs

Frameshift

Pathogenic

NA

NA

26

Exon6

NM_000532.5:c.634G > T

p.Asp212Tyr

Missense

Early

Likely Pathogenic

29.6

20

[118]

Poor feeding, hypotonia, pancytopenia, hyperlactatemia

l-carnitine, vitamin B12, special milk powder, a restricted protein diet

Development delay, intellectual disability

 

Exon8

NM_000532.5:c.838dup

p.Leu280fs

Frameshift

Pathogenic

NA

NA

27

Exon3

NM_000532.5:c.359_360delAT

p.Tyr120Cysfs*40

Frameshift

Early

Likely Pathogenic

NA

NA

[7]

Recurrent infections, diarrhea, metabolic acidosis, and generalized tonic–clonic seizures

Low isoleucine, methionine, threonine and proline diet with the supplementation of l-carnitine and biotin

Moderate intellectual disability and development delay

 

Intron13

NM_000532.5:c.1398 + 1G > A

NA

Splice site mutation

Likely Pathogenic

35

20

28

Exon13

NM_000532.5:C.1381G > C

p.Ala461Pro

Missense

Early

Likely Pathogenic

30

20

[66]

Vomiting

Special milk powder and oral administration of l-carnitine from 100 to 200 mg/kg every day

NA

 

Exon13

NM_000532.5:c.1301C > T

p.Ala434Val

Missense

Pathogenic

32

20

29

Exon13

NM_000532.5:C.1381G > C

p.Ala461Pro

Missense

Early

Likely Pathogenic

30

20

Poor feeding

NA

Died due to severe multiple organ failure

 

Exon13

NM_000532.5:c.1301C > T

p.Ala434Val

Missense

Pathogenic

32

20

30

Exon15

NM_000532.5:c.1535G > A

p.Arg512His

Missense

Early

Pathogenic

31

20

Poor feeding, lethargy, coma, hypotonia, metabolic acidosis and hyperammonemia

NA

Died from a severe multiple organ failure after the discharge requested by the parents at twenty-four days old

 

Exon15

NM_000532.5:c.1535G > A

p.Arg512His

Missense

Pathogenic

31

20

31

Exon11

NM_000532.5:c.1131dup

p.Val378Cysfs*5

Frameshift

Early

Likely Pathogenic

NA

NA

[119]

Lethargy, irregular breathing, with groaning and snoring, hypotonia, non-rosy skin, hypoglycemia, and metabolic acidosis

NA

Died due to respiratory failure

 

Exon1

NM_000532.5:c.-10_183 + 10del203

NA

Deletion mutation

NA

NA

NA

32

Exon11

NM_000532.5:c.1131dup

p.Val378Cysfs*5

Frameshift

Early

Likely Pathogenic

NA

NA

NA

 

Exon1

NM_000532.5:c.-10_183 + 10del203

NA

Deletion mutation

NA

NA

NA

33

Exon8

NM_000532.5:c.838dup

p.Leu280ProfsTer11

Frameshift

Early

Pathogenic

NA

NA

Poor feeding, hypotonia, sepsisticemia, and multiple organ failure

NA

Died at seven days old after birth

 

Exon11

NM_000532.5:C.1098G > C

P.Leu366Phe

Missense

Likely Pathogenic

25.8

20

34

Intron14

NM_000532.5:c.1498 + 1G > A

NA

Splice site mutation

Early

Likely Pathogenic

34

20

NA

NA

Died shortly after birth due to metabolic abnormalities

 

Intron14

NM_000532.5:c.1498 + 1G > A

NA

Splice site mutation

Likely Pathogenic

34

20

35

Exon2

NM_000532.5:c.224A > C

p.Asp75Ala

Missense

Newborn screening

Likely Pathogenic

29.9

20

[114]

NA

NA

NA

 

Exon13

NM_000532.5:c.1339C > T

p.Leu447Phe

Missense

Uncertain Significance

25.5

20

36

Exon13

NM_000532.5:c.1301C > T

p.Ala434Val

Missense

Early

Pathogenic

32

20

[107]

Jaundice, hyperammonemia, and metabolic acidosis

Special milk powder and supplementation of l-carnitine

Regular follow-up revealed mild development delay and intellectual disability

 

Exon10

NM_000532.5:c.1087 T > C

p.Ser363Pro

Missense

Likely Pathogenic

30

20

  1. NA, not available; MSC, Mutation Significance Cutoff