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Table 2 Pathogenic and likely pathogenic variants classified by ACMG-AMP guidelines

From: Genetic epidemiology of autoinflammatory disease variants in Indian population from 1029 whole genomes

Gene

Variant

SNPID

Protein change

ACMG criteria

Classification

Inheritance

Disease

ADAR

chr1:154602065:G>C

rs145588689

c.C577G: p.P193A

PM1, PP3, PM3, PP4

Likely pathogenic 5

AR

AGS

IL36RN

chr2:113060943:T:C

rs148755083

c.115+6T>C: p.Arg10ArgfsX1

PS2, PS3, PP5

Pathogenic 2

AR

DITRA

IL36RN

chr2:113062547:C>T

rs144478519

c.C338T: p.S113L

PM1, PP3, PS3, PM3, PP1, PP4

Pathogenic 3b

AR

DITRA

AP1S3

chr2:223777862:A>C

rs116107386

c.T11G: p.F4C

PM1, PP3, PS3, BS4

Likely pathogenic 2

AD

Pustular psoriasis

RNASEH2C

chr11:65720385:G>A

rs78635798

c.C205T: p.R69W

PM1, PM2, PP3, PP5, PS3, PP1-M

Pathogenic 3a

AR

AGS

MVK

chr12:109586107:A>G

rs104895364

c.A613G: p.N205D

PM1, PM2, PP3, PP4

Likely pathogenic 5

AR

HIDS

MVK

chr12:109596515:G>A

rs28934897

c.G1129A: p.V377I

BP4, PS4, PM3, PP1-M

Likely pathogenic 2

AR

HIDS

RNASEH2B

chr13:50945445:G>A

rs75184679

c.G529A: p.A177T

PM1, PP3, PP5, PS3, BS3, PP4

Likely pathogenic 2

AR

AGS

PSTPIP1

chr15:77031192:C:T

rs751668240

c.C850T: p.Q284X

PVS1, PM2, PP3

Pathogneic 1c

AD

PAPA

NOD2

chr16:50711206:C>T

rs2076754

c.C1295T: p.A432V

PM1, PM2, PP3, BS3, PS4

Likely pathogenic 2

AD

Blau Syndrome

NOD2

chr16:50711301:G>T

rs104895492

c.G1390T: p.G464W

PM2, PP3, PS3, PP1

Likely pathogenic 2

AD

Blau Syndrome

NOD2

chr16:50712048:C>T

rs104895440

c.C2137T: p.R713C

PM2, PP3, PS3

Likely pathogenic 2

AD

Blau Syndrome

CARD14

chr17:80184015:G>A

rs200731780

c.G452A: p.R151Q

PM2, BP4, PS3

Likely pathogenic 2

AD

CAMPS

CARD14

chr17:80198685:C:T

rs200379060

c.C1234T: p.R412X

PVS1, PM2

Likely pathogenic 1

AD

CAMPS

NLRP7

chr19:54936400:G>A

rs104895525

c.C2161T: p.R721W

PM2, PP3, PS1

Likely pathogenic 2

AR

HYDM1

NLRP12

chr19:53810605:G:A

rs199881207

c.C1054T: p.R352C

PM1, PM2, PS3, PP3

Likely pathogenic 2

AD

FACS

ADA2

chr22:17203564:G>A

rs148936893

c.C626T: p.P209L

PM1, PM2, BP4, PP5, PS3, PM3, PP1

Pathogenic 3a

AR

DADA2

ADA2

chr22:17209538:C>A

rs200930463

c.G140T: p.G47V

PM1, PM2, PP3, PP5, PM5

Likely pathogenic 4

AR

DADA2

ADA2

chr22:17209539:C>G

rs202134424-G

c.G139C: p.G47R

PM1, PM2, PP3, PS1, PS3, PS4

Pathogenic 2

AR

DADA2

ADA2

chr22:17209539:C>T

rs202134424-T

c.G139A: p.G47R

PM1, PM2, PP3, PP5, PS3, PS4

Pathogenic 2

AR

DADA2

  1. AGS Aicardi-Goutières syndrome, DITRA deficiency of interleukin-36-receptor antagonist, HIDS hyper IgD syndrome, CAMPS CARD14-mediated pustular psoriasis, HYDM1 hydatidiform mole, recurrent, 1, DADA2 deficiency of adenosine deaminase 2, AR autosomal recessive, AD autosomal dominant