Skip to main content

Table 1 Characteristics and the pathogenicity prediction of the identified variant

From: A novel missense variant in ESRRB gene causing autosomal recessive non-syndromic hearing loss: in silico analysis of a case

Features of the reported variant

 

Gene symbol

ESRRB

Locus

DFNB35

Nucleotide acid change

c.499G>A

Ref SNP Id

rs1555342141

Protein change

p.G167R

Domain

DBD

Co-segregation

Yes

Frequency in the control population of this study

0.000

ACMG/AMP criteria

PM5, PM1, PM2, PP1, PP3

 

Variant pathogenicity prediction

Web servers

Values

Pathogenicity

PolyPhen2

Probably damaging (0.997)

SIFT

Deleterious (0.0)

FATHMM

Damaging (− 6.21)

MutationAssessor

High (3.65)

MutationTaster

Disease-causing (1.000)

LOFtool

Probably damaging (0.193)

MetaSVM

Deleterious (0.911)

LRT

Deleterious (0.62918)

GERP++

Damaging (5.12)

MAF

1000 Genomes

0.000

ESP

0.000

ExAC

0.000

Conservation

UniProtKB/UniRef100

Yes

Protein stability

SDM

Destabilizing

MAESTROweb

Destabilizing

  1. The Polymorphism phenotyping v2 (PolyPhen-2) scores range from 0.0 (tolerated) to 1.0 (deleterious). The Sorting Intolerant from Tolerant (SIFT) values range from 0 to 1. The variant is predicted damaging if the score is ≤ 0.05, and tolerated if the score is > 0.05. The Functional Analysis through Hidden Markov Models (FATHMM) scores range from − 16.13 to 10.64. The smaller the score the more likely the variant has a damaging effect. If a FATHMM score is ≤  − 1.5 the corresponding variant is predicted as "D(AMAGING)"; on the contrary, it is predicted as "T(OLERATED)". MutationAssessor scores range from 5.135 to 6.49. MutationAssessor's functional impact of a variant: predicted functional, i.e. high ("H") or medium ("M"), or predicted non-functional, i.e. low ("L") or neutral ("N"). MutationTaster score ranges from 0 to 1 and a larger score means more likely to be deleterious. MutationTaster predictions are "A" ("disease_causing_automatic"), "D" ("disease_causing"), "N" ("polymorphism") or "P" ("polymorphism_automatic"). The Loss-of-function (LOF) tool scores < 0.7 are considered benign, scores < 0.2 are considered probably damaging and a score of 0.2 to 0.7 are possibly damaging. The Meta Support Vector Machine (MetaSVM) score ranges from − 2 to 3 and the larger scores indicate the variant is more likely to be damaging. The likelihood ratio test (LRT) ranges from 0 to 1 and the LRT predictions are D(eleterious), N(eutral), or U(nknown). Genomic Evolutionary Rate Profiling (tmGERP)++ scores range from − 12.3 to 6.71, where a larger score indicates deleterious variation. ACMG/AMP, American College of Medical Genetics and Genomics/Association for Molecular Pathology; MAF, Minor Allele Frequency; ESP, Exome Sequencing Project; ExAC, Exome Aggregation Consortium; SDM, Site Directed Mutator; SNP, Single Nucleotide Polymorphism
Back to article page

BMC Medical Genomics

ISSN: 1755-8794

Contact us