chr12-7831752-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PP3_Moderate
The NM_001286234.2(SLC2A14):c.124T>C(p.Phe42Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000372 in 1,614,144 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: 𝑓 0.000013 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000027 ( 0 hom. )
Consequence
SLC2A14
NM_001286234.2 missense
NM_001286234.2 missense
Scores
3
8
5
Clinical Significance
Conservation
PhyloP100: 8.12
Genes affected
SLC2A14 (HGNC:18301): (solute carrier family 2 member 14) Members of the glucose transporter (GLUT) family, including SLC2A14, are highly conserved integral membrane proteins that transport hexoses such as glucose and fructose into all mammalian cells. GLUTs show tissue and cell-type specific expression (Wu and Freeze, 2002 [PubMed 12504846]).[supplied by OMIM, Mar 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PP3
?
MetaRNN computational evidence supports a deleterious effect, 0.847
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC2A14 | NM_001286234.2 | c.124T>C | p.Phe42Leu | missense_variant | 4/11 | ENST00000431042.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC2A14 | ENST00000431042.7 | c.124T>C | p.Phe42Leu | missense_variant | 4/11 | 1 | NM_001286234.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152260Hom.: 0 Cov.: 33
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GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461884Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 727244
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GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152260Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74390
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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 | Feb 09, 2023 | The c.193T>C (p.F65L) alteration is located in exon 5 (coding exon 3) of the SLC2A14 gene. This alteration results from a T to C substitution at nucleotide position 193, causing the phenylalanine (F) at amino acid position 65 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Benign
Cadd
Uncertain
Dann
Uncertain
Eigen
Uncertain
Eigen_PC
Benign
FATHMM_MKL
Pathogenic
D
M_CAP
Benign
D
MetaRNN
Pathogenic
D;D;D;D;D;D;D;D;D;D;D;D;D
MetaSVM
Uncertain
D
MutationTaster
Benign
D;D;D;D;N;N;N;N;N
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;.;D;D;D;D;D;D;D;D;D;D;D
REVEL
Uncertain
Sift
Benign
D;.;D;D;D;D;T;D;T;D;D;D;D
Sift4G
Uncertain
D;D;D;D;D;D;T;.;T;.;T;.;.
Polyphen
P;D;D;P;D;.;.;.;.;.;.;.;.
Vest4
MutPred
0.69
.;Gain of catalytic residue at I61 (P = 0.0159);Gain of catalytic residue at I61 (P = 0.0159);.;Gain of catalytic residue at I61 (P = 0.0159);.;.;.;.;Gain of catalytic residue at I61 (P = 0.0159);Gain of catalytic residue at I61 (P = 0.0159);.;.;
MVP
MPC
0.88
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