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Table 3 Likely pathogenic variants in MYH15, CSP1, and MYH3

From: Novel potential causative genes in carotid paragangliomas

Gene

rs ID number

GenBank

Coordinate

Nucleotide change

Amino acid change

Genotype/number of samples

Predictions

SIFT

PolyPhen2

MutationTaster

LRT

CPS1

–

–

Chr2: 211494571

c.2706-7855G > A

–

Het/2

N/A

N/A

N/A

N/A

–

–

Chr2: 211494681

c.2706-7745C > G

–

Het/1

N/A

N/A

N/A

N/A

–

–

Chr2: 211494618

c.2706-7798delA

–

Het/1

N/A

N/A

N/A

N/A

–

NM_001122633.2

Chr2: 211539650

c.4144G > A

p.Gly1382Ser

Het/2

Tolerated

Benign

Disease-causing

Deleterious

MYH15

rs56118396

NM_014981.1

Chr3: 108112954

c.5243G > A

p.Arg1748Gln

Het/4

Tolerated

Benign

Disease-causing

N/A

–

Chr3: 108110666

c.5431G > A

p.Glu1811Lys

Het/1

Deleterious

Probably damaging

Disease-causing

N/A

MYH3

rs34088014

NM_002470.3

Chr17: 10542709

c.3008C > T

p.Ala1003Val

Het/2

Tolerated

Benign

Disease-causing

N/A

rs61735358

Chr17: 10541497

c.3592G > A

p.Ala1198Thr

Het/1

Tolerated

Possibly damaging

Disease-causing

N/A

rs201488879

Chr17: 10535939

c.4810G > A

p.Ala1604Thr

Het/1

Deleterious

Possibly damaging

Disease-causing

N/A

rs34393601

Chr17: 10534960

c.5254G > A

p.Ala1752Thr

Het/3

Deleterious

Possibly damaging

Disease-causing

N/A

rs763347751

Chr17: 10550688

c.791 T > C

p.Ile264Thr

Het/1

Deleterious

Probably damaging

Disease-causing

N/A

rs746986821

Chr17: 10543684

c.2392A > G

p.Met798Val

Het/1

Deleterious

Benign

Possibly disease-causing

N/A

rs551363957

Chr17: 10541370

c.3719C > T

p.Ser1240Leu

Het/1

Deleterious

Benign

Disease-causing

N/A

rs769788909

Chr17: 10547753

c.1325C > T

p.Thr442Ile

Het/1

Tolerated

Benign

Possibly disease-causing

N/A

  1. SIFT scores range from 0 to 1, and variants with SIFT scores less than 0.05 are considered deleterious. SIFT scores ranging from 0.05 to 1 are predicted to be tolerated variants
  2. The PolyPhen-2 scores range from 0 to 1. Variants with scores ranging from 0 to 0.15 in this range are predicted to be benign. Variants with scores ranging from 0.15 to 0.85 are potential damaging, whereas values above 0.85 have higher probability of being damaging variants
  3. MutationTaster p-values (probability) range from 0 to 1. P-values close to 1 indicate pathogenicity (disease-causing)
  4. LRT is a likelihood ratio test. LRT scores range from 0 (neutral) to 1 (deleterious)
  5. Het heterozygous genotype