rs776087207

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_006931.3(SLC2A3):​c.1435G>T​(p.Gly479Cys) 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. 16/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G479S) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 33)

Consequence

SLC2A3
NM_006931.3 missense

Scores

19

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.486
Variant links:
Genes affected
SLC2A3 (HGNC:11007): (solute carrier family 2 member 3) Enables dehydroascorbic acid transmembrane transporter activity; glucose binding activity; and glucose transmembrane transporter activity. Involved in glucose import across plasma membrane and transport across blood-brain barrier. Is integral component of plasma membrane. Biomarker of Alzheimer's disease; acanthosis nigricans; diabetes mellitus; and type 2 diabetes mellitus. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.08628926).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SLC2A3NM_006931.3 linkc.1435G>T p.Gly479Cys missense_variant Exon 10 of 10 ENST00000075120.12 NP_008862.1 P11169

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SLC2A3ENST00000075120.12 linkc.1435G>T p.Gly479Cys missense_variant Exon 10 of 10 1 NM_006931.3 ENSP00000075120.7 P11169

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
35
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
0.11
BayesDel_addAF
Benign
-0.11
T
BayesDel_noAF
Benign
-0.40
CADD
Benign
7.6
DANN
Benign
0.96
DEOGEN2
Benign
0.18
T
Eigen
Benign
-1.2
Eigen_PC
Benign
-1.3
FATHMM_MKL
Benign
0.057
N
LIST_S2
Benign
0.16
T
M_CAP
Benign
0.040
D
MetaRNN
Benign
0.086
T
MetaSVM
Benign
-0.68
T
MutationAssessor
Benign
0.0
N
PrimateAI
Benign
0.28
T
PROVEAN
Benign
-1.1
N
REVEL
Benign
0.20
Sift
Benign
0.048
D
Sift4G
Benign
0.16
T
Polyphen
0.32
B
Vest4
0.16
MutPred
0.35
Gain of catalytic residue at K477 (P = 0.0511);
MVP
0.18
MPC
1.4
ClinPred
0.24
T
GERP RS
-1.6
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1
Varity_R
0.072
gMVP
0.53

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
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: rs776087207; hg19: chr12-8074065; API