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Table 2 Variations detected in type Ia, type Ib and type II Brazilian MSUD patients

From: Maple syrup urine disease in Brazilian patients: variants and clinical phenotype heterogeneity

Spot

Nucleotide change

Protein prediction

Type

Prediction of pathogenicity

Classification

ACMG classification

Referenceb

Frequency (patients)

SIFT®

Polyphen-2®

MutPred®

BCKDHA gene

 Promoter

c.109-3575_288 + 4del

p.(?)

SS

Damaging

Feier et al. [15]

1/21

 Exon 2

c.116C > A

p.(Pro39His)

M

Non-damaging

Non-damaging

Non-damaging

Non-damaging

Henneke et al. [25]c

5/21

 Exon 2

c.116C > T

p.(Pro39Leu)

M

Non-damaging

Non-damaging

Non-damaging

Non-damaging

Uncertain significance PP2/PP3/PM2

This studya

1/21

 Exon 2

c.166G > C

p.(Gly56Arg)

M

Damaging

Damaging

Non-damaging

Non-Damaging

Uncertain significance PP2/PP3/PM2

This study

2/21

 Exon 3

c.357_358delCT

p.(Tyr120Ter)

D

Damaging

Phatogenic PVS1/PP3/PM2

This study

1/21

 Exon 4

c.454G > A

p.(Asp152Ans)

M

Damaging

Damaging

Damaging

Damaging

Quental et al. [17]

1/21

 Exon 6

c.659C > T

p.(Ala220Val)

M

Damaging

Damaging

Damaging

Damaging

Rodriguez-Pombo et al. [9]

1/21

 Exon 6

c.740_741insT

p.(Ala248Cysfs * 10)

I

Damaging

DB

2/21

 Exon 7

c.859C > T

p.(Arg287Ter)

N

Damaging

Chinsky et al. [37]

1/21

BCKDHB gene

 Exon 1

c.92_102dup11

p.(Phe35Trpfs * 41)

Dup

Damaging

Rodriguez-Pombo et al. [9]

1/21

 Exon 1

c.188_189delinsCA

p.(Arg63Pro)

M

Non-damaging

Non-damaging

Non-damaging

Non-damaging

Uncertain significance BP4/PM2/PP2

This study

1/21

 Intron 3

c.343 + 2 T > G

p.(?)

SS

Damaging

Feier et al. [15]

1/21

 Exon 4

c.392G > T

p.(Gly131Val)

M

Damaging

Damaging

Damaging

Damaging

Uncertain significance PP2/PP3/PM2

This study

2/21

 Exon 4

c.436delinsCA

p.(Glu146Glnfs * 13)

D/I

Damaging

Pathogenic PVS1/PP3/PM2

This study

1/21

 Exon 4

c.445_446delTT

p.(Phe149Cysfs * 9)

D

Damaging

Pathogenic PVS1/PP3/PM2

This study

1/21

 Exon 5

c.498G > C

p.(Lys166Asn)

M

Damaging

Damaging

Damaging

Damaging

Scaini et al. [38]

1/21

 Exon 5

c.502C > T

p.(Arg168Cys)

M

Damaging

Damaging

Damaging

Damaging

Flaschker et al. [34]

1/21

 Exon 5

c.506A > G

p.(Tyr169Cys)

M

Damaging

Damaging

Damaging

Damaging

DB

1/21

 Exon 5

c.595_596delAG

p.(Pro200Ter)

D

Damaging

Henneke et al. [25]

4/21

 Exon 5

c.605C > T

p.(Ala202Val)

M

Damaging

Damaging

Damaging

Damaging

DB

1/21

 Exon 5

c.620G > T

p.(Cys207Phe)

M

Damaging

Damaging

Non-damaging

Damaging

Uncertain significance PP2/PP3/PM2

This studya

1/21

 Exon 5

c.633G > C

p.(Lys211Asn)

M

Damaging

Damaging

Damaging

Damaging

Uncertain significance PP2/PP3/BP6

This studya

1/21

 Exon 6

c.641T > A

p.(Ile214Lys)a

M

Damaging

Damaging

Damaging

Damaging

Rodriguez-Pombo et al. [9]

2/21

 Exon 7

c.743delC

p.(Ala248Glyfs * 6)

D

Damaging

Feier et al. [15]

2/21

 Exon 7 + Intron 7

c.764_840 + 4del;840 + 9_ + 22delf

?

D

Damaging

Feier et al. [15]

2/21

 Exon 8

c.853C > T

p.(Arg285Ter)e

N

Damaging

Henneke et al. [25]

1/21

DBT gene

 Exon 4

c.346G > A

p.(Gly116Arg)

M

Damaging

Damaging

Damaging

Damaging

Scaini et al. [38]

2/21

 Exon 5

c.442G > T

p.(Glu148Ter)

N

Damaging

Pathogenic PVS1/PP3/PP5/PM2

This study

2/21

 Exon 9

c.1150A > G

p.(Ser384Gly)

M

Non-damaging

Non-damaging

Non-damaging

Non-damaging

Tsuruta et al. [35]d

2/21

 Exon 10

c.1250A > T

p.(Glu417Val)

M

Damaging

Damaging

Damaging

Damaging

Uncertain significance PP3/PM2

This study

1/21

  1. M missense, Dup duplication, D deletion, I insertion, N nonsense, SS splice site, DB database
  2. aNew mutation related to MSUD, however presented in data banks
  3. bMutation Database HGMD (The Human Gene Mutation Database) and Mutation Taster
  4. cThe mutation is probably a polymorphism, previously named T106M (Dursun et al. [39])
  5. dNon damaging mutation previously named G323S (Tsuruta et al. [35])
  6. eThe variation of nucleotide sequency have not been identified at the genomic level; at cDNA level, the effect is the 3’UTR site alteration
  7. fWe have also identified these two variants occurring together