rs1888055214

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3

The NM_024884.3(L2HGDH):​c.1271G>C​(p.Gly424Ala) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,866 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic 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 š‘“: 6.8e-7 ( 0 hom. )

Consequence

L2HGDH
NM_024884.3 missense

Scores

8
5
6

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 7.88
Variant links:
Genes affected
L2HGDH (HGNC:20499): (L-2-hydroxyglutarate dehydrogenase) This gene encodes L-2-hydroxyglutarate dehydrogenase, a FAD-dependent enzyme that oxidizes L-2-hydroxyglutarate to alpha-ketoglutarate in a variety of mammalian tissues. Mutations in this gene cause L-2-hydroxyglutaric aciduria, a rare autosomal recessive neurometabolic disorder resulting in moderate to severe cognitive disability. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 3 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.824

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
L2HGDHNM_024884.3 linkc.1271G>C p.Gly424Ala missense_variant Exon 10 of 10 ENST00000267436.9 NP_079160.1 Q9H9P8-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
L2HGDHENST00000267436.9 linkc.1271G>C p.Gly424Ala missense_variant Exon 10 of 10 1 NM_024884.3 ENSP00000267436.4 Q9H9P8-1
L2HGDHENST00000261699.8 linkc.1197-9454G>C intron_variant Intron 9 of 9 1 ENSP00000261699.4 C9JVN9
L2HGDHENST00000421284.7 linkc.1271G>C p.Gly424Ala missense_variant Exon 10 of 11 2 ENSP00000405559.3 Q9H9P8-1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
AF:
6.84e-7
AC:
1
AN:
1461866
Hom.:
0
Cov.:
32
AF XY:
0.00
AC XY:
0
AN XY:
727234
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000252
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

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.20
BayesDel_addAF
Pathogenic
0.41
D
BayesDel_noAF
Pathogenic
0.36
CADD
Pathogenic
26
DANN
Uncertain
1.0
DEOGEN2
Uncertain
0.46
T;T
Eigen
Pathogenic
0.75
Eigen_PC
Pathogenic
0.75
FATHMM_MKL
Pathogenic
0.99
D
LIST_S2
Uncertain
0.97
.;D
M_CAP
Benign
0.082
D
MetaRNN
Pathogenic
0.82
D;D
MetaSVM
Uncertain
0.64
D
MutationAssessor
Benign
1.8
L;L
PrimateAI
Uncertain
0.50
T
PROVEAN
Pathogenic
-5.6
D;D
REVEL
Pathogenic
0.88
Sift
Benign
0.11
T;T
Sift4G
Benign
0.10
T;T
Polyphen
0.94
P;P
Vest4
0.72
MutPred
0.59
Gain of catalytic residue at D422 (P = 2e-04);Gain of catalytic residue at D422 (P = 2e-04);
MVP
0.90
MPC
0.83
ClinPred
0.99
D
GERP RS
5.3
Varity_R
0.60
gMVP
0.83

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.020
Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr14-50713897; API