Table 1 Harmful prediction of the five novel variants in MSX1

From: Novel MSX1 variants identified in families with nonsyndromic oligodontia

Families

Exon

Nucleotide

change

Protein

change

Variation

type

ExAC (MAF)

SIFT

PolyPhen-2

Mutation

Taster

ACMG classification (evidence of pathogenicity)

Family 1

1

c.364G>T

p.G122*

Nonsense

—

  

Disease

causing

Pathogenic

(PVS1 + PM2 + PM5 + PP1)

Family 2

1

c.277delG

p.A93Rfs*67

Frameshift

—

  

Disease

causing

Pathogenic

(PVS1 + PM2 + PP3)

Family 3

2

c.809C>T

p.S270L

Missense

—

0.057

(tolerated)

0.213

(benign)

Disease

causing

Uncertain significance

(PM2 + PP3)

Family 4

2

c.662A>C

p.Q221P

Missense

—

0.032

(damaging)

1.000

(probably damaging)

Disease

causing

Likely Pathogenic

(PS2 + PM2 + PP1 + PP3)

Family 5

2

c.670C>T

p.R224C

Missense

4.012 × 10−6

0.000

(damaging)

0.998

(probably damaging)

Disease

causing

Uncertain significance

(PP1 + PP3)

  1. Note: — variant was not found in ExAC
  2. ACMG, American College of Medical Genetics; PM, pathogenic criterion is weighted as moderate; PP, pathogenic as strong; PVS, pathogenic criterion is weighted as very strong
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