Table 3 Reported pathogenic mt-tRNA variants with discordant evaluation.

From: Interpretation of mitochondrial tRNA variants

Position

Gene

Nucleotide change

MitoTIP score

Location

Reported

Re-evaluation

Added criteria by our cases

Criteria

Before addition of new cases

After addition of new cases

616

MT-TF

T>C

17.5

ACS

P

LP

P

PS5

PS5, PM7, PM9, PM10

5540

MT-TW

G>A

16.1

ACS

P

LP

P

PM8, PM9

PS3, PM7, PM8, PM9, PP4, PP6

8362

MT-TK

T>G

18.6

AS

P

LP

P

PM9

PS3, PM7, PM9, PP4, PP6

15915

MT-TT

G>A

16.1

ACS

P

LP

P

PS5

PS5, PM7, PM8, PM9, PM10

618

MT-TF

T>C

14.8

ACS

P

LP

LP

 

PM5, PM8, PM9, PP3

1624

MT-TV

C>T

15.3

DS

P

LP

LP

 

PS3, PP3, PP4

1630

MT-TV

A>G

16.7

ACS

P

LP

LP

 

PS3, PM7, PP4, PP6

1659

MT-TV

T>C

15.5

TS

P

LP

LP

PM8

PM8, PM9, PP3, PP6

3242

MT-TL1

G>A

7

DS

P

LP

LP

 

PS5, PM9, PM10

3252

MT-TL1

A>G

11.5

DL

P

LP

LP

PM9

PM8, PM9, PM10

3288

MT-TL1

A>G

10.9

TL

P

LP

LP

PM9

PM8, PM9, PP4, PP6

4284

MT-TI

G>A

10.7

C2

P

LP

LP

PM9

PM8, PM9, PM10

4296

MT-TI

G>A

12.4

ACL

P

LP

LP

PM8, PM10

PM8, PM9, PM10

4308

MT-TI

G>A

17.3

TS

P

LP

LP

 

PM7, PM8, PM9, PM10, PP6

8299

MT-TK

G>A

14.4

AS

P

LP

LP

 

PM8, PM10, PP3, PP6

9997

MT-TG

T>A

19.6

AS

P

LP

LP

PM9

PM5, PM7, PM9, PM10

10406

MT-TR

G>A

16

AS

P

LP

LP

 

PM7, PM8, PM9, PM10

12264

MT-TS2

C>T

16.7

AS

P

LP

LP

 

PM7, PM9, PM10

14674

MT-TE

T>C

9.6

DB

P

LP

LP

 

PS5, PP4, PP6

14709

MT-TE

T>C

13

ACL

P

LP

LP

 

PS5, PP3, PP4, PP6

15995

MT-TP

G>A

16.9

ACS

P

LP

LP

 

PM7, PM9, PP4, PP6

16002

MT-TP

T>C

16.3

DS

P

LP

LP

 

PM7, PM8, PM9, PP6

1643

MT-TV

A>G

11.9

VR

P

VUS

VUS

 

PM10, PP6

3250

MT-TL1

T>C

10.3

DL

P

VUS

VUS

 

PM8, PP6, BS4

4290

MT-TI

T>C

12.5

ACL

P

VUS

VUS

BS4

PP3, BS4

4320

MT-TI

C>T

17.9

TS

P

VUS

VUS

BP6

PM7, BP6

5559

MT-TW

A>G

15.5

TS

P

VUS

VUS

PM9

PM9, PP3, PP6

5693

MT-TN

T>C

9.9

ACL

P

VUS

VUS

 

PS3, BP4

7520

MT-TD

G>A

13

AS

P

VUS

VUS

 

PP3

12293

MT-TL2

G>A

15

ACS

P

VUS

VUS

BP5

PP3, PP6, BP5

15950

MT-TT

G>A

12.9

AS

P

VUS

VUS

BP6

PP3, BP6

16018

MT-TP

ins15

 

AS

P

VUS

VUS

BP6

BP6

3275

MT-TL1

C>A

2

VR

P

VUS

LB

BS4

BS4, BP4

3236

MT-TL1

A>G

11.2

AS

P

VUS

B

BS2

BS1, BS2

4381

MT-TQ

A>G

5.4

DL

P

LB

B

BS4

BS1, BS4, BP4

15926

MT-TT

C>T

1.1

ACS

P

LB

B

BS2

BS1, BS2, BP4

12148a

MT-TH

T>C

16.2

DS

VUS

VUS

LP

PM9, PP4, PP6

PM7, PM9, PP4, PP6

  1. ACL anticodon loop,ACS anticodon stem, AS acceptor stem, B benign, C1 connector 1, C2 connector 2, DB discriminator base, DL D loop, DS D stem, LB likely benign, LP likely pathogenic, mt-tRNA mitochondrial transfer RNA,P pathogenic, TL T loop, TS T stem, VR variable region, VUS variant of uncertain significance.
  2. aThe only VUS upgraded to LP.
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