1-9010199-C-T
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Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_207420.3(SLC2A7):c.1060G>A(p.Gly354Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00000572 in 1,399,492 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.0000057 ( 0 hom. )
Consequence
SLC2A7
NM_207420.3 missense
NM_207420.3 missense
Scores
6
9
4
Clinical Significance
Conservation
PhyloP100: 6.47
Genes affected
SLC2A7 (HGNC:13445): (solute carrier family 2 member 7) SLC2A7 belongs to a family of transporters that catalyze the uptake of sugars through facilitated diffusion (Li et al., 2004). This family of transporters shows conservation of 12 transmembrane helices as well as functionally significant amino acid residues (Joost and Thorens, 2001 [PubMed 11780753]).[supplied by OMIM, Mar 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.984
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC2A7 | NM_207420.3 | c.1060G>A | p.Gly354Ser | missense_variant | 9/12 | ENST00000400906.2 | |
SLC2A7 | XM_011540824.3 | c.1060G>A | p.Gly354Ser | missense_variant | 9/12 | ||
SLC2A7 | XM_011540825.3 | c.1060G>A | p.Gly354Ser | missense_variant | 9/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC2A7 | ENST00000400906.2 | c.1060G>A | p.Gly354Ser | missense_variant | 9/12 | 1 | NM_207420.3 | P1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
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33
GnomAD3 exomes AF: 0.00000647 AC: 1AN: 154468Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 81814
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GnomAD4 exome AF: 0.00000572 AC: 8AN: 1399492Hom.: 0 Cov.: 33 AF XY: 0.00000435 AC XY: 3AN XY: 690302
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GnomAD4 genome Cov.: 33
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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 submitter | clinical testing | Ambry Genetics | Oct 02, 2023 | The c.1060G>A (p.G354S) alteration is located in exon 9 (coding exon 9) of the SLC2A7 gene. This alteration results from a G to A substitution at nucleotide position 1060, causing the glycine (G) at amino acid position 354 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Uncertain
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D
M_CAP
Uncertain
D
MetaRNN
Pathogenic
D
MetaSVM
Uncertain
D
MutationAssessor
Benign
L
MutationTaster
Benign
D
PrimateAI
Benign
T
PROVEAN
Pathogenic
D
REVEL
Pathogenic
Sift
Pathogenic
D
Sift4G
Pathogenic
D
Polyphen
D
Vest4
MutPred
Loss of catalytic residue at G354 (P = 0.0768);
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at