GeneBe

1-42929016-TCG-CCT

Variant names:
GermlineCancer (beta)

Variant summary

Our verdict is Uncertain significance.
+1 Uncertain · Cold
-7
-6
-1
0
+5
+6
+9
+10
B
LB
VUS
LP
P
 The variant received 1 classification points (ACGS-UK Somatic Oncogenicity v2025). O3_ModerateB4_Supporting

The NM_006516.4(SLC2A1):c.988_990delCGAinsAGG (p.331) variant causes a synonymous change. The gene SLC2A1 is a tumor suppressor gene (CancerMine: 3 TSG, 14 oncogene, 1 driver citations). The gene SLC2A1 is a known oncogene (CancerMine: 3 TSG, 14 oncogene, 1 driver citations). The gene SLC2A1 is a cancer driver gene (CancerMine: 3 TSG, 14 oncogene, 1 driver citations). Note: allele frequency estimates from gnomAD may be inaccurate for this variant type (MNP or indel longer than 3 bp) due to technology limitations. The variant is absent from the gnomAD population database at sites with sufficient sequencing coverage. The affected nucleotide is highly conserved across species (PhyloP 100-way vertebrate score: 7.52). No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 33)

Consequence

SLC2A1
NM_006516.4 synonymous

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 7.52

Publications

0 publications found
Variant links:
Genes affected
SLC2A1 (HGNC:11005): (solute carrier family 2 member 1) This gene encodes a major glucose transporter in the mammalian blood-brain barrier. The encoded protein is found primarily in the cell membrane and on the cell surface, where it can also function as a receptor for human T-cell leukemia virus (HTLV) I and II. Mutations in this gene have been found in a family with paroxysmal exertion-induced dyskinesia. [provided by RefSeq, Apr 2013]
SLC2A1 Gene-Disease associations (from GenCC):
  • encephalopathy due to GLUT1 deficiency
    Inheritance: AD, AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Orphanet, G2P
  • GLUT1 deficiency syndrome
    Inheritance: SD, AD Classification: DEFINITIVE, STRONG Submitted by: PanelApp Australia, ClinGen
  • childhood onset GLUT1 deficiency syndrome 2
    Inheritance: AD Classification: STRONG, SUPPORTIVE Submitted by: Genomics England PanelApp, Orphanet
  • dystonia 9
    Inheritance: AD Classification: STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Genomics England PanelApp, Orphanet
  • epilepsy, idiopathic generalized, susceptibility to, 12
    Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
  • childhood absence epilepsy
    Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
  • hereditary cryohydrocytosis with reduced stomatin
    Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
  • myoclonic-astatic epilepsy
    Inheritance: Unknown Classification: SUPPORTIVE Submitted by: Orphanet

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript NM_006516.4, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

Classification according to ACGS-UK Somatic Oncogenicity v2025

Classification was made for transcript:

Our verdict: Uncertain_significance. The variant received 1 points.

O3Absent or very rare in population
Absent or extremely rare in gnomAD (AC ≤ 2) — O3 moderate; GnomAD: AF = absent, AC = 0 — absent/extremely rare (O3 moderate [+2])
B4Synonymous/intronic, no splicing impact
Synonymous/intronic variant outside canonical splice sites (B4 supporting); Synonymous variant — splicing impact not confirmed absent; B4 supporting [-1]

Variant Effect in Transcripts

Automated classification analysis was done for transcript: NM_006516.4. You can select a different transcript below to see updated classification assignments.

RefSeq Transcripts

SLC2A1 NM_006516.4
MANE Select
HGVSc / HGVSpc.988_990delCGAinsAGGp.331
Exon rankN/A
synonymous
Prot: NP_006507.2UniProt: P11166

Ensembl Transcripts

SLC2A1 ENST00000426263.10
TSL:1MANE Select
HGVSc / HGVSpc.988_990delCGAinsAGGp.331
Exon rankN/A
synonymous
Prot: ENSP00000416293.2UniProt: P11166
SLC2A1 ENST00000889577.1
HGVSc / HGVSpc.985_987delCGAinsAGGp.330
Exon rankN/A
synonymous
Prot: ENSP00000559636.1UniProt: A0ACI8RFT3
SLC2A1 ENST00000958848.1
HGVSc / HGVSpc.988_990delCGAinsAGGp.331
Exon rankN/A
synonymous
Prot: ENSP00000628907.1UniProt: A0ACI8V0G7

Frequencies

Allele frequencies (AF), counts (AC/AN), homozygotes and coverage

Common (AF > 0.05 / Hom > 5)
Rare (AF ≤ 0.0001 / Hom ≤ 1)
Global population databases 2 sources
GnomAD3 genomes
Cov:33
GnomAD4 genome
Cov:33
Showing 2 sources
Tested, but no data found:GnomAD4 exomeIf GnomAD4 is missing, the position is probably not covered by the project.

ClinVar

Not reported in ClinVar

Computational Scores

PhyloP100
Pathogenic7.5
Showing 1 of 1 scores

Splicing Scores

No splicing scores have been computed for this variant.

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

MaveDB functional evidence

MaveDB is a public repository of laboratory assays that test the effect of thousands of variants at once — treat this as supporting research data and interpret it with great caution; it is not a clinical classification.

No MaveDB functional evidence found for this variant.

Publications

Other links and lift over

hg19: chr1-43394687;
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