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Table 3 (Likely) pathogenic variants in non-BMPR2 genes

From: Gene panel diagnostics reveals new pathogenic variants in pulmonary arterial hypertension

Gene

Exon

DNA

Protein

CADD score

GnomAD count

Diagnosis

ACVRL1

3

c.205T > C

p.(Cys69Arg)

25

0

HPAH (HHT)

ACVRL1

5

c.578T > C

p.(Leu193Pro)

31

0

HPAH (HHT)

ACVRL1

10

c.1450C > T

p(Arg484Trp)

26

0

HPAH

AQP1

1

c.376C > T

p.(Arg126Cys)

26

0

HPAH

ATP13A3

14

c.1540C > T

p.(Gln514*)

NA (Nonsense)

0

Drugs and toxins induced PAH [17]

EIF2AK4

1

c.1A > T

p.(Met1?)b

NA (Start loss)

0

PVOD

EIF2AK4

6

c.595-1G > A

intronic b

35

0

PVOD

EIF2AK4

6

c.641delA

p.(Lys241Argfs*21)a

NA (Deletion)

0

PVOD

EIF2AK4

9

c.1362C > A

p.(Cys454*)b

NA (Nonsense)

0

CTD-APAH

EIF2AK4

21

c.2965C > T

p.(Arg989Trp)b

31

5

PVOD

EIF2AK4

24

c.3380C > T

p.(Ala1127Val)b

26

0

PVOD

EIF2AK4

25

c.3443T > C

p.(Leu1148Ser)b

31

0

CTD-APAH

EIF2AK4

31

c.4260G > A

p.(Trp1420*)a

NA (Nonsense)

0

PVOD

ENG

12

c.1646G > A

p.(Cys549Tyr)

26

0

IPAH

GDF2

2

c.857dupA

p.(Leu287Alafs*11)

NA (Duplication)

0

IPAH

GDF2

1

c.329G > A

p.(Arg110Gln)

32

0

HPAH

KCNK3

2

c.641T > C

p.(Leu214Pro)

27

0

IPAH

KCNK3

2

c.340G > A

p.(Ala114Thr)

26

0

HPAH

KCNK3

1

c.250_267dup TTCTACTTCGCCATCACC

p.(Val84_Thr89dup)a

NA (Duplication)

0

HPAH

SMAD9

2

c.29T > C

p.(Leu10Pro)

27

0

HPAH

SOX17

1

c.273_277delAGACC

p.(Asp92Alafs*68)

NA (Deletion)

0

IPAH

SOX17

2

c.413G > C

p.(Arg138Pro)

33

0

HPAH

SOX17

2

c.1245A > G

p.(*415Trp)

Stop loss

0

CHD-APAH

SOX17

2

c.499_520del

p.(Leu167Trpfs*213)

NA (Deletion)

0

IPAH

TBX4

2

c.278G > A

p.(Gly93Asp)

33

0

IPAH

TBX4

3

c.400delT

p.(Trp134Glyfs*38)

NA (Deletion)

0

IPAH

TBX4

6

c.709_710ins56bp

p.(Gln237Profs*18)b

NA (Insertion)

0

IPAH

TBX4

8

c.1543G > A

p.(Glu515Lys)b

24

0

IPAH

  1. aHomozygous variant
  2. bTogether with 2nd variant in same gene
  3. APAH associated pulmonary arterial hypertension; CADD score Combined Annotation Dependent Depletion score, summation score based on different in silico prediction programmes, CHD congenital heart disease, CTD connective tissue disease, GnomAD Genome Aggregation Consortium Database with n = 125,748 samples, HHT hereditary haemorrhagic telangiectasia, HPAH heritable pulmonary arterial hypertension, IPAH idiopathic pulmonary arterial hypertension, PVOD pulmonary veno-occlusive disease. Used Ensembl transcripts and respective reference sequences: ACVRL1: ENST00000267008.3, NM_000020; AQP1: ENST00000311813.11, NM_198098.3; ATP13A3: ENST00000256031.4, NM_024524.3; EIF2AK4: ENST00000263791.1 NM_001013703; ENG: ENST00000373203.2, NM_001114753; GDF2: ENST00000249598, NM_016204.2; KCNK3: ENST00000302909, NM_002246.2; SMAD9: ENST00000379826.1, NM_001127217; SOX17: ENST00000297316, NM_022454.3; TBX4: ENST00000240335.1, NM_018488.3