NM_003041.4:c.178C>G

Variant summary

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

The NM_003041.4(SLC5A2):ā€‹c.178C>Gā€‹(p.Arg60Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000656 in 152,338 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: š‘“ 0.0000066 ( 0 hom., cov: 32)

Consequence

SLC5A2
NM_003041.4 missense

Scores

2
10
7

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0610
Variant links:
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]

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 rank MANE Protein UniProt
SLC5A2NM_003041.4 linkc.178C>G p.Arg60Gly missense_variant Exon 2 of 14 ENST00000330498.4 NP_003032.1 P31639-1
SLC5A2XM_006721072.5 linkc.178C>G p.Arg60Gly missense_variant Exon 2 of 13 XP_006721135.3 Q8WY15
SLC5A2XM_024450402.2 linkc.178C>G p.Arg60Gly missense_variant Exon 2 of 11 XP_024306170.2
SLC5A2NR_130783.2 linkn.192C>G non_coding_transcript_exon_variant Exon 2 of 12

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SLC5A2ENST00000330498.4 linkc.178C>G p.Arg60Gly missense_variant Exon 2 of 14 1 NM_003041.4 ENSP00000327943.3 P31639-1

Frequencies

GnomAD3 genomes
AF:
0.00000657
AC:
1
AN:
152220
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0000241
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD4 exome
Cov.:
32
GnomAD4 genome
AF:
0.00000656
AC:
1
AN:
152338
Hom.:
0
Cov.:
32
AF XY:
0.0000134
AC XY:
1
AN XY:
74492
show subpopulations
Gnomad4 AFR
AF:
0.0000241
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.41
BayesDel_addAF
Pathogenic
0.35
D
BayesDel_noAF
Pathogenic
0.27
CADD
Uncertain
25
DANN
Uncertain
1.0
DEOGEN2
Benign
0.079
T;T
Eigen
Uncertain
0.36
Eigen_PC
Uncertain
0.29
FATHMM_MKL
Benign
0.35
N
LIST_S2
Benign
0.63
T;T
M_CAP
Uncertain
0.19
D
MetaRNN
Uncertain
0.72
D;D
MetaSVM
Uncertain
0.55
D
MutationAssessor
Benign
1.3
.;L
PrimateAI
Uncertain
0.48
T
PROVEAN
Uncertain
-4.2
D;D
REVEL
Uncertain
0.63
Sift
Benign
0.086
T;T
Sift4G
Benign
0.11
T;T
Polyphen
1.0
.;D
Vest4
0.69
MVP
0.95
MPC
0.93
ClinPred
0.98
D
GERP RS
4.1
Varity_R
0.75
gMVP
0.93

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.26
Details are displayed if max score is > 0.2
DS_DL_spliceai
0.26
Position offset: 20

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: rs201586410; hg19: chr16-31496045; COSMIC: COSV100393412; COSMIC: COSV100393412; API