3-171014511-G-C

Variant summary

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

The NM_000340.2(SLC2A2):​c.329C>G​(p.Thr110Ser) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/21 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. T110I) has been classified as Benign.

Frequency

Genomes: not found (cov: 32)

Consequence

SLC2A2
NM_000340.2 missense

Scores

1
4
14

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 7.13
Variant links:
Genes affected
SLC2A2 (HGNC:11006): (solute carrier family 2 member 2) This gene encodes an integral plasma membrane glycoprotein of the liver, islet beta cells, intestine, and kidney epithelium. The encoded protein mediates facilitated bidirectional glucose transport. Because of its low affinity for glucose, it has been suggested as a glucose sensor. Mutations in this gene are associated with susceptibility to diseases, including Fanconi-Bickel syndrome and noninsulin-dependent diabetes mellitus (NIDDM). Alternative splicing results in multiple transcript variants of this gene. [provided by RefSeq, Jul 2013]

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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=0.22531426).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SLC2A2NM_000340.2 linkc.329C>G p.Thr110Ser missense_variant Exon 3 of 11 ENST00000314251.8 NP_000331.1 P11168-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SLC2A2ENST00000314251.8 linkc.329C>G p.Thr110Ser missense_variant Exon 3 of 11 1 NM_000340.2 ENSP00000323568.3 P11168-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
33
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.13
BayesDel_addAF
Benign
-0.12
T
BayesDel_noAF
Benign
-0.41
CADD
Benign
22
DANN
Uncertain
0.99
DEOGEN2
Benign
0.40
T
Eigen
Benign
-0.24
Eigen_PC
Benign
0.0047
FATHMM_MKL
Uncertain
0.87
D
LIST_S2
Uncertain
0.90
D
M_CAP
Benign
0.042
D
MetaRNN
Benign
0.23
T
MetaSVM
Benign
-0.84
T
MutationAssessor
Benign
0.27
N
PrimateAI
Benign
0.48
T
PROVEAN
Benign
-1.1
N
REVEL
Benign
0.24
Sift
Pathogenic
0.0
D
Sift4G
Uncertain
0.0030
D
Polyphen
0.0070
B
Vest4
0.089
MutPred
0.64
Gain of disorder (P = 0.0361);
MVP
0.79
MPC
0.13
ClinPred
0.63
D
GERP RS
6.1
Varity_R
0.27
gMVP
0.59

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.050
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: chr3-170732300; API