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Egyptian Journal of Medical Human Genetics

Table 2 Genotype and phenotype characteristics in those who underwent WES

From: Genetic testing and family screening in idiopathic pediatric cardiomyopathy: a prospective observational study from a tertiary care center in North India

SN

Age (months)/gender

Diagnosis

Current Status

Result of whole-exome sequencing

AGGRESCAN

PhosphoSite

SpliceAILookup

Conservation score

Coordinate

Amino acid change

Type of variant

ACMG variant classification

PhyloP100way

Pathogenic and likely pathogenic variants (P/LP)

1

48/F

DCM

Deceased

chr11:47,364,158 C > -

MYBPC3(NM_000256.3):c.1595del(p.Gly532AlafsTer23)

Frameshift deletion

P

0

No

No

7.234, 5.542, −3.35

1, 7.234, 7.234

2

12/F

DCM

Alive

chr11:47,357,555 G > -

MYBPC3(NM_000256.3):c.2610del(p.Ser871AlafsTer8)

Frameshift deletion

P

0

No

No

−0.511, 9.426, 3.950, 1.163, 8.735, 5.972

3

9/M

DCM

Deceased

chr11:47,357,555 G > -

MYBPC3(NM_000256.3):c.2610del(p.Ser871AlafsTer8)

Frameshift deletion

P

0

No

No

−0.511, 9.426, 3.950, 1.163, 8.735, 5.973

4

8/M

DCM

Deceased

chr16:46,766,372 G > A

MYLK3(NM_182493.3):c.1210C > T(p.Gln404Ter)

Nonsense mutation

LP

 − 8.7

No

No

0.832

5

9/M

DCM

Lost to follow-up

chr18:19,751,370 G > -

GATA6(NM_005257.6):c.268del(p.Ala90LeufsTer47)

Frameshift deletion

LP

0

No

No

5.388, 2.644, 0.797, 1.053

Variants of unknown significance (VUS)

6

23/M

DCM with non-compaction

Alive

chr11:47,365,047 C > T

MYBPC3(NM_000256.3):c.1219G > A(p.Gly407Ser)

Missense mutation

VUS

0

Phosphorylation on S406 and S408

Donor loss—0.04—0 bp, Donor Gain—0.04—-4 bp

5.454

7

54/F

DCM with non-compaction

Alive

chr2:179,496,966 G > A

TTN(NM_001267550.2):c.43655C > T(p.Ser14552Leu)

Missense mutation

VUS

NA

Ubiquitination on R14553

Donor Gain—0.13—36 bp

5.57

8

13/M

DCM

Lost to follow-up

chr2:220,283,700 GC > -

DES(NM_001927.4):c.525_526del(p.Val176ArgfsTer48)

Frameshift deletion

VUS

0

No

Donor Gain—0.04—-18 bp

4.168, 3.658, 6.527, −0.140, 2.346, 5.820, −0.336, 2.916, 9.537, −0.508, 7.699

9

15/M

DCM

Deceased

chr6:7,566,613 C > T

DSP(NM_004415.4):c.943C > T(p.Arg315Cys)

Missense mutation

VUS

0.1

No

No

6.999

  1. The identified variants have been listed along with the HGVS nomenclature, ACMG classification, and corresponding valid rule and supporting information from other computational prediction tools, i.e., AGGRESCAN, PhospoSite, and SpliceAILookup. Detailed scores of all computational tools obtained from Varsome are included in Table S2 in the Additional file 1 to support its pathogenicity. AGGRESCAN is a web-based software used for the prediction of aggregation-prone regions in protein sequences, the analysis of the effect of variants on protein aggregation tendencies, and for the comparison of the aggregation properties of different proteins. Negative values suggest low aggregation propensity, and vice versa for positive values. PhosphoSite is a curated, web-based bioinformatics resource devoted to protein phosphorylation sites in human and mouse genomes. It provides information about the phosphorylated amino acid and its surrounding sequence, location of the site within known domains and motifs, orthologous sites in other species, as well as relevant literature references. SpliceAILookup is an open-source deep learning-based splicing prediction tool used to identify splice variants and annotates genetic variants with their predicted effect on splicing. PhyloP100way scores are based on multiple alignments of 99 vertebrate genome sequences to the human genome. The higher the score, the more conserved the site
  2. DCM Dilated cardiomyopathy, MYBPC myosin-binding protein C, MYLK myosin light chain kinase, GATA6 GATA-binding protein 6, TTN titin, DES desmin, DSP desmoplakin, P pathogenic, LP likely pathogenic, VUS variant of unknown significance
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