rs202201763

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 3P and 2B. PM2PP5BP4BS1_Supporting

The NM_020442.6(VARS2):​c.1168G>A​(p.Ala390Thr) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000183 in 1,540,782 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: 𝑓 0.00037 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00016 ( 0 hom. )

Consequence

VARS2
NM_020442.6 missense, splice_region

Scores

6
6
7

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:8U:4

Conservation

PhyloP100: 8.79
Variant links:
Genes affected
VARS2 (HGNC:21642): (valyl-tRNA synthetase 2, mitochondrial) This gene encodes a mitochondrial aminoacyl-tRNA synthetase, which catalyzes the attachment of valine to tRNA(Val) for mitochondrial translation. Mutations in this gene cause combined oxidative phosphorylation deficiency-20, and are also associated with early-onset mitochondrial encephalopathies. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Aug 2014]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 6-30920091-G-A is Pathogenic according to our data. Variant chr6-30920091-G-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 522814.We mark this variant Likely_pathogenic, oryginal submissions are: {Likely_pathogenic=2, Pathogenic=3, Uncertain_significance=4}. Variant chr6-30920091-G-A is described in Lovd as [Pathogenic].
BP4
Computational evidence support a benign effect (MetaRNN=0.10521114). . Strength limited to SUPPORTING due to the PP5.
BS1
Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.000374 (57/152304) while in subpopulation AMR AF= 0.00235 (36/15308). AF 95% confidence interval is 0.00175. There are 0 homozygotes in gnomad4. There are 32 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
VARS2NM_020442.6 linkc.1168G>A p.Ala390Thr missense_variant, splice_region_variant Exon 13 of 30 ENST00000676266.1 NP_065175.4 Q5ST30-1B4E0K6B4DG77
VARS2NM_001167734.2 linkc.1258G>A p.Ala420Thr missense_variant, splice_region_variant Exon 13 of 30 NP_001161206.1 Q5ST30-4A0A1U9X9B3
VARS2NM_001167733.3 linkc.748G>A p.Ala250Thr missense_variant, splice_region_variant Exon 12 of 29 NP_001161205.1 Q5ST30-3B4E0K6

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
VARS2ENST00000676266.1 linkc.1168G>A p.Ala390Thr missense_variant, splice_region_variant Exon 13 of 30 NM_020442.6 ENSP00000502585.1 Q5ST30-1

Frequencies

GnomAD3 genomes
AF:
0.000375
AC:
57
AN:
152186
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.000121
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00235
Gnomad ASJ
AF:
0.000288
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000176
Gnomad OTH
AF:
0.00143
GnomAD3 exomes
AF:
0.000402
AC:
76
AN:
188830
Hom.:
0
AF XY:
0.000407
AC XY:
41
AN XY:
100740
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00232
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000181
Gnomad OTH exome
AF:
0.000662
GnomAD4 exome
AF:
0.000162
AC:
225
AN:
1388478
Hom.:
0
Cov.:
51
AF XY:
0.000149
AC XY:
102
AN XY:
683432
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00235
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000119
Gnomad4 OTH exome
AF:
0.000314
GnomAD4 genome
AF:
0.000374
AC:
57
AN:
152304
Hom.:
0
Cov.:
33
AF XY:
0.000430
AC XY:
32
AN XY:
74464
show subpopulations
Gnomad4 AFR
AF:
0.000120
Gnomad4 AMR
AF:
0.00235
Gnomad4 ASJ
AF:
0.000288
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000176
Gnomad4 OTH
AF:
0.00142
Alfa
AF:
0.000207
Hom.:
0
Bravo
AF:
0.000646
ESP6500AA
AF:
0.00
AC:
0
ESP6500EA
AF:
0.000185
AC:
1
ExAC
AF:
0.000277
AC:
33

ClinVar

Significance: Conflicting classifications of pathogenicity
Submissions summary: Pathogenic:8Uncertain:4
Revision: criteria provided, conflicting classifications
LINK: link

Submissions by phenotype

Combined oxidative phosphorylation defect type 20 Pathogenic:4Uncertain:1
May 28, 2019
Mendelics
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

May 04, 2017
Undiagnosed Diseases Network, NIH
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

This variant was found in trans with another variant (c.1076-14A>G) in a 6-year-old male with severe neurodevelopmental impairment, encephalopathy, microcephaly, hypertrophic cardiomyopathy, lactic acidosis, seizure disorder (infantile spasms), abnormal MRI showing brain and brainstem atrophy. -

Feb 22, 2021
Department of Pediatrics, Salzburger Landeskliniken & Paracelsus Medical University
Significance: Pathogenic
Review Status: no assertion criteria provided
Collection Method: clinical testing

- -

Jul 10, 2020
OMIM
Significance: Pathogenic
Review Status: no assertion criteria provided
Collection Method: literature only

- -

Dec 18, 2023
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Significance: Likely pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

Variant summary: VARS2 c.1168G>A (p.Ala390Thr) results in a non-conservative amino acid change located in the Aminoacyl-tRNA synthetase, class Ia domain (IPR002300) of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. Consensus agreement among computation tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 0.00018 in 1534628 control chromosomes (gnomAD V4.0). The variant, c.1168G>A (aka. c.1258G>A, p.Ala420Thr), has been reported in the literature in multiple individuals affected with Combined Oxidative Phosphorylation Defect Type 20 (Bruni_2018, Kusikova_2021). One of these publications reported that VARS2 protein was deficient in patient derived muscle biopsy, and the resulting defect of oxidative phosphorylation was also demonstrated by enzymatic assay (Kusikova_2021). These data indicate that the variant is very likely to be associated with disease. The following publications have been ascertained in the context of this evaluation (PMID: 29314548, 33937156, 34216551). 11 submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. Multiple submitters reported the variant with conflicting assessments. Based on the evidence outlined above, the variant was classified as likely pathogenic. -

not provided Pathogenic:3Uncertain:1
Nov 22, 2024
GeneDx
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 33937156, 34484863, 31623496, 30458719, 34216551, 29314548, 38752301) -

Aug 01, 2022
CeGaT Center for Human Genetics Tuebingen
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

VARS2: PM3, PM2:Supporting -

Jan 23, 2025
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

This sequence change replaces alanine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 420 of the VARS2 protein (p.Ala420Thr). This variant is present in population databases (rs202201763, gnomAD 0.2%). This missense change has been observed in individual(s) with clinical features of VARS2-related conditions (PMID: 29314548, 33937156; internal data). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 522814). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. For these reasons, this variant has been classified as Pathogenic. -

Apr 01, 2024
Mayo Clinic Laboratories, Mayo Clinic
Significance: Likely pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

PP4, PM3, PS4 -

VARS2-related disorder Pathogenic:1
Jun 03, 2024
PreventionGenetics, part of Exact Sciences
Significance: Likely pathogenic
Review Status: no assertion criteria provided
Collection Method: clinical testing

The VARS2 c.1258G>A variant is predicted to result in the amino acid substitution p.Ala420Thr. This variant was reported in the homozygous state in two siblings and an apparently unrelated individual with VARS2-related mitochondrial disease (Bruni et al. 2018. PubMed ID: 29314548). This variant was also reported, with alternative nomenclature (NM_020442.6:c.1168G>A; p.Ala390Thr), in the compound heterozygous state in another individual with a similar phenotype (Kušíková et al. 2021. PubMed ID: 33937156). Experimental studies on muscle homogenate from that patient indicated that VARS2 protein was deficient. This variant is reported in 0.24% of alleles in individuals of Latino descent in gnomAD. This variant is interpreted as likely pathogenic. -

Inborn genetic diseases Uncertain:1
Aug 11, 2021
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

Bruni, 2018 Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

See cases Uncertain:1
Dec 18, 2020
Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

ACMG classification criteria: BS1 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.30
BayesDel_addAF
Benign
-0.16
T
BayesDel_noAF
Uncertain
-0.010
CADD
Pathogenic
32
DANN
Pathogenic
1.0
DEOGEN2
Benign
0.25
T;.;.
Eigen
Pathogenic
0.86
Eigen_PC
Pathogenic
0.75
FATHMM_MKL
Pathogenic
1.0
D
LIST_S2
Pathogenic
0.99
D;D;D
M_CAP
Benign
0.042
D
MetaRNN
Benign
0.11
T;T;T
MetaSVM
Benign
-0.34
T
MutationAssessor
Pathogenic
3.9
H;.;.
PrimateAI
Uncertain
0.68
T
PROVEAN
Uncertain
-3.5
D;.;D
REVEL
Uncertain
0.49
Sift
Uncertain
0.0020
D;.;D
Sift4G
Uncertain
0.010
D;D;D
Polyphen
1.0
D;.;.
Vest4
0.65
MVP
0.76
MPC
1.3
ClinPred
0.31
T
GERP RS
4.8
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.89
gMVP
0.87

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.13
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs202201763; hg19: chr6-30887868; COSMIC: COSV100422929; COSMIC: COSV100422929; API