2-63597407-G-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_005917.4(MDH1):​c.208G>T​(p.Ala70Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 33)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

MDH1
NM_005917.4 missense

Scores

6
13

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.53
Variant links:
Genes affected
MDH1 (HGNC:6970): (malate dehydrogenase 1) This gene encodes an enzyme that catalyzes the NAD/NADH-dependent, reversible oxidation of malate to oxaloacetate in many metabolic pathways, including the citric acid cycle. Two main isozymes are known to exist in eukaryotic cells: one is found in the mitochondrial matrix and the other in the cytoplasm. This gene encodes the cytosolic isozyme, which plays a key role in the malate-aspartate shuttle that allows malate to pass through the mitochondrial membrane to be transformed into oxaloacetate for further cellular processes. Alternatively spliced transcript variants have been found for this gene. A recent study showed that a C-terminally extended isoform is produced by use of an alternative in-frame translation termination codon via a stop codon readthrough mechanism, and that this isoform is localized in the peroxisomes. Pseudogenes have been identified on chromosomes X and 6. [provided by RefSeq, Feb 2016]
WDPCP (HGNC:28027): (WD repeat containing planar cell polarity effector) This gene encodes a cytoplasmic WD40 repeat protein. A similar gene in frogs encodes a planar cell polarity protein that plays a critical role in collective cell movement and ciliogenesis by mediating septin localization. Mutations in this gene are associated with Bardet-Biedl syndrome 15 and may also play a role in Meckel-Gruber syndrome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jun 2014]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MDH1NM_005917.4 linkc.208G>T p.Ala70Ser missense_variant Exon 4 of 9 ENST00000233114.13 NP_005908.1 P40925-1V9HWF2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MDH1ENST00000233114.13 linkc.208G>T p.Ala70Ser missense_variant Exon 4 of 9 1 NM_005917.4 ENSP00000233114.8 P40925-1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
1274892
Hom.:
0
Cov.:
30
AF XY:
0.00
AC XY:
0
AN XY:
623176
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
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:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
33
Bravo
AF:
0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.21
BayesDel_addAF
Benign
0.0082
T
BayesDel_noAF
Benign
-0.23
CADD
Uncertain
23
DANN
Uncertain
0.99
DEOGEN2
Uncertain
0.65
D;T;.;T;.
Eigen
Benign
-0.066
Eigen_PC
Benign
0.017
FATHMM_MKL
Uncertain
0.95
D
LIST_S2
Benign
0.84
T;T;T;T;T
M_CAP
Uncertain
0.092
D
MetaRNN
Benign
0.34
T;T;T;T;T
MetaSVM
Uncertain
-0.038
T
MutationAssessor
Benign
1.9
M;.;.;.;.
PrimateAI
Benign
0.36
T
PROVEAN
Benign
-1.6
N;N;N;N;N
REVEL
Uncertain
0.37
Sift
Benign
0.13
T;D;T;T;T
Sift4G
Benign
0.21
T;T;T;T;T
Polyphen
0.018
B;.;.;.;.
Vest4
0.27
MutPred
0.56
Loss of ubiquitination at K66 (P = 0.0561);.;.;.;.;
MVP
0.82
MPC
0.28
ClinPred
0.57
D
GERP RS
3.6
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.037
gMVP
0.35

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.51
Details are displayed if max score is > 0.2
DS_AG_spliceai
0.51
Position offset: 7

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: rs533261577; hg19: chr2-63824541; API