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GeneBe

12-40048181-T-C

Variant summary

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

The NM_052885.4(SLC2A13):c.586A>G(p.Ile196Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000384 in 1,459,930 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 0.000038 ( 0 hom. )

Consequence

SLC2A13
NM_052885.4 missense

Scores

1
10
8

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 7.39
Variant links:
Genes affected
SLC2A13 (HGNC:15956): (solute carrier family 2 member 13) Enables ATPase binding activity; myo-inositol:proton symporter activity; and protease binding activity. Involved in myo-inositol transport and positive regulation of amyloid-beta formation. Is integral component of plasma membrane. Part of cell body; cell periphery; and cell projection. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

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/exons MANE UniProt
SLC2A13NM_052885.4 linkuse as main transcriptc.586A>G p.Ile196Val missense_variant 2/10 ENST00000280871.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SLC2A13ENST00000280871.9 linkuse as main transcriptc.586A>G p.Ile196Val missense_variant 2/101 NM_052885.4 P1
SLC2A13ENST00000380858.1 linkuse as main transcriptc.586A>G p.Ile196Val missense_variant 2/41

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD3 exomes
AF:
0.0000162
AC:
4
AN:
247152
Hom.:
0
AF XY:
0.0000225
AC XY:
3
AN XY:
133568
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
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:
0.0000356
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000384
AC:
56
AN:
1459930
Hom.:
0
Cov.:
31
AF XY:
0.0000358
AC XY:
26
AN XY:
726234
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000477
Gnomad4 OTH exome
AF:
0.0000497
GnomAD4 genome
Cov.:
32
Bravo
AF:
0.00000378
ExAC
AF:
0.0000165
AC:
2

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsJan 26, 2023The c.586A>G (p.I196V) alteration is located in exon 2 (coding exon 2) of the SLC2A13 gene. This alteration results from a A to G substitution at nucleotide position 586, causing the isoleucine (I) at amino acid position 196 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.20
BayesDel_addAF
Uncertain
0.035
T
BayesDel_noAF
Uncertain
-0.080
Cadd
Benign
23
Dann
Uncertain
1.0
DEOGEN2
Benign
0.17
T;T
Eigen
Uncertain
0.54
Eigen_PC
Uncertain
0.60
FATHMM_MKL
Pathogenic
0.98
D
LIST_S2
Uncertain
0.91
D;D
M_CAP
Benign
0.021
T
MetaRNN
Uncertain
0.49
T;T
MetaSVM
Uncertain
-0.26
T
MutationAssessor
Benign
0.90
L;.
MutationTaster
Benign
1.0
D;D
PrimateAI
Uncertain
0.68
T
PROVEAN
Benign
-0.60
N;N
REVEL
Uncertain
0.36
Sift
Benign
0.26
T;T
Sift4G
Benign
0.22
T;T
Polyphen
0.88
P;P
Vest4
0.57
MutPred
0.49
Gain of glycosylation at S200 (P = 0.1337);Gain of glycosylation at S200 (P = 0.1337);
MVP
0.49
MPC
0.63
ClinPred
0.43
T
GERP RS
5.7
Varity_R
0.15
gMVP
0.32

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: rs758683743; hg19: chr12-40441983; API