16-31483183-A-G

Variant names:

• chr16-31483183-A-G
• NM_003041.4:c.47A>G

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_003041.4(SLC5A2):​c.47A>G​(p.Gln16Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: SLC5A2 NM_003041.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 2.79

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.20412311).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC5A2	NM_003041.4	c.47A>G	p.Gln16Arg	missense_variant	Exon 1 of 14	ENST00000330498.4	NP_003032.1
SLC5A2	XM_006721072.5	c.47A>G	p.Gln16Arg	missense_variant	Exon 1 of 13		XP_006721135.3
SLC5A2	XM_024450402.2	c.47A>G	p.Gln16Arg	missense_variant	Exon 1 of 11		XP_024306170.2
SLC5A2	NR_130783.2	n.61A>G		non_coding_transcript_exon_variant	Exon 1 of 12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC5A2	ENST00000330498.4	c.47A>G	p.Gln16Arg	missense_variant	Exon 1 of 14	1	NM_003041.4	ENSP00000327943.3
SLC5A2	ENST00000419665.6	n.47A>G		non_coding_transcript_exon_variant	Exon 1 of 12	1		ENSP00000410601.2
SLC5A2	ENST00000569576.5	c.-4+115A>G		intron_variant	Intron 1 of 4	4		ENSP00000455143.1
SLC5A2	ENST00000562006.1	n.46A>G		non_coding_transcript_exon_variant	Exon 1 of 3	3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

Familial renal glucosuria Uncertain:1

Apr 07, 2024

Fulgent Genetics, Fulgent Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.069
BayesDel_addAF	Benign	-0.052	T
BayesDel_noAF	Benign	-0.31
CADD	Benign	16
DANN	Benign	0.46
DEOGEN2	Benign	0.13	T
Eigen	Benign	-0.81
Eigen_PC	Benign	-0.71
FATHMM_MKL	Benign	0.54	D
LIST_S2	Benign	0.54	T
M_CAP	Benign	0.084	D
MetaRNN	Benign	0.20	T
MetaSVM	Benign	-0.79	T
MutationAssessor	Benign	1.2	L
PrimateAI	Benign	0.43	T
PROVEAN	Benign	-0.15	N
REVEL	Benign	0.14
Sift	Benign	0.57	T
Sift4G	Benign	0.67	T
Polyphen		0.012	B
Vest4		0.43
MutPred		0.23		Gain of loop (P = 0.0312);
MVP		0.64
MPC		0.25
ClinPred		0.055	T
GERP RS		2.8
Varity_R		0.025
gMVP		0.40

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr16-31494504;