chr16-31484885-G-A
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Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PP3_StrongPP5
The NM_003041.4(SLC5A2):c.265G>A(p.Ala89Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000753 in 1,461,788 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 Pathogenic (no stars).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000075 ( 0 hom. )
Consequence
SLC5A2
NM_003041.4 missense
NM_003041.4 missense
Scores
14
3
2
Clinical Significance
Conservation
PhyloP100: 9.97
Genes affected
SLC5A2 (HGNC:11037): (solute carrier family 5 member 2) This gene encodes a member of the sodium glucose cotransporter family which are sodium-dependent glucose transport proteins. The encoded protein is the major cotransporter involved in glucose reabsorption in the kidney. Mutations in this gene are associated with renal glucosuria. Two transcript variants, one protein-coding and one not, have been found for this gene. [provided by RefSeq, Feb 2015]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 5 ACMG points.
PP3
MetaRNN computational evidence supports a deleterious effect, 0.98
PP5
Variant 16-31484885-G-A is Pathogenic according to our data. Variant chr16-31484885-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 253135.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC5A2 | NM_003041.4 | c.265G>A | p.Ala89Thr | missense_variant | 3/14 | ENST00000330498.4 | |
SLC5A2 | XM_006721072.5 | c.265G>A | p.Ala89Thr | missense_variant | 3/13 | ||
SLC5A2 | XM_024450402.2 | c.265G>A | p.Ala89Thr | missense_variant | 3/11 | ||
SLC5A2 | NR_130783.2 | n.279G>A | non_coding_transcript_exon_variant | 3/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC5A2 | ENST00000330498.4 | c.265G>A | p.Ala89Thr | missense_variant | 3/14 | 1 | NM_003041.4 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
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32
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251172Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135784
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GnomAD4 exome AF: 0.00000753 AC: 11AN: 1461788Hom.: 0 Cov.: 32 AF XY: 0.00000688 AC XY: 5AN XY: 727202
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GnomAD4 genome Cov.: 32
GnomAD4 genome
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32
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Familial renal glucosuria Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Aug 02, 2016 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Pathogenic
DEOGEN2
Benign
T;T
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Pathogenic
D;D
M_CAP
Pathogenic
D
MetaRNN
Pathogenic
D;D
MetaSVM
Pathogenic
D
MutationAssessor
Pathogenic
.;H
MutationTaster
Benign
D
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;D
REVEL
Pathogenic
Sift
Pathogenic
D;D
Sift4G
Uncertain
D;D
Polyphen
1.0
.;D
Vest4
0.94
MutPred
0.93
.;Gain of phosphorylation at A89 (P = 0.0977);
MVP
MPC
0.80
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