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Table 2 Summary of the pathogenicity predictions of the TSAG10 variant

From: A novel homozygous TSGA10 missense variant causes acephalic spermatozoa syndrome in a Pakistani family

Gene

TSAG10

Mutation position

Mutation type

Missense

Exon

15

cDNA

c.1112T > C

Protein

p. L371P

Prediction

Score / % Expected accuracy

SIFTa

 Affect protein function

0.01

PolyPhen-2b

 Probably damaging

1.000

PolyPhen-1

 Deleterious

74%

PredictSNPc

 Deleterious

61%

PANTHERd

 Deleterious

74%

MAPPe

 Deleterious

84%

SNAPf

 Deleterious

81%

  1. aSIFT: (Stop, Investigate, Find, Trace) assigns scores closer to 0.00 to SNPs that are more likely to be damaging)
  2. bPolyPhen-2: (Polymorphism Phenotyping) provides a score between 0 and 1, with scores closer to 1 indicating a higher confidence in predicting the SNP as damaging)
  3. cPredictSNP: (Used for prediction of the effects of mutation on protein function)
  4. dPANTHER: (Protein analysis through evolutionary relationships)
  5. eMAPP: (Multivariate Analysis of Protein Polymorphism) A method that aims to predict the deleteriousness of non-synonymous single nucleotide polymorphisms)
  6. fSNAP: (Scala Nucleotide Alignment Polymorphism)
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Basic and Clinical Andrology

ISSN: 2051-4190