19-49430725-C-T

Variant names:

• chr19-49430725-C-T
• NM_020309.4:c.1477G>A

Variant summary

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

The NM_020309.4(SLC17A7):​c.1477G>A​(p.Glu493Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: SLC17A7 NM_020309.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 7.90

Genes affected

SLC17A7 (HGNC:16704): (solute carrier family 17 member 7) The protein encoded by this gene is a vesicle-bound, sodium-dependent phosphate transporter that is specifically expressed in the neuron-rich regions of the brain. It is preferentially associated with the membranes of synaptic vesicles and functions in glutamate transport. The protein shares 82% identity with the differentiation-associated Na-dependent inorganic phosphate cotransporter and they appear to form a distinct class within the Na+/Pi cotransporter family. [provided by RefSeq, Jul 2008]

ACMG classification

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
SLC17A7	NM_020309.4	c.1477G>A	p.Glu493Lys	missense_variant	Exon 12 of 12	ENST00000221485.8	NP_064705.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC17A7	ENST00000221485.8	c.1477G>A	p.Glu493Lys	missense_variant	Exon 12 of 12	1	NM_020309.4	ENSP00000221485.2
SLC17A7	ENST00000600601.5	c.1276G>A	p.Glu426Lys	missense_variant	Exon 12 of 12	2		ENSP00000470338.1
SLC17A7	ENST00000600672.5	n.*30G>A		downstream_gene_variant		5

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Jan 10, 2022

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.1477G>A (p.E493K) alteration is located in exon 12 (coding exon 12) of the SLC17A7 gene. This alteration results from a G to A substitution at nucleotide position 1477, causing the glutamic acid (E) at amino acid position 493 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.72
BayesDel_addAF	Uncertain	0.15	D
BayesDel_noAF	Uncertain	-0.020
CADD	Pathogenic	32
DANN	Pathogenic	1.0
DEOGEN2	Pathogenic	0.81	D;.
Eigen	Uncertain	0.42
Eigen_PC	Uncertain	0.49
FATHMM_MKL	Uncertain	0.95	D
LIST_S2	Pathogenic	0.99	D;D
M_CAP	Benign	0.078	D
MetaRNN	Uncertain	0.71	D;D
MetaSVM	Benign	-0.62	T
MutationAssessor	Benign	1.9	L;.
PrimateAI	Pathogenic	0.81	D
PROVEAN	Uncertain	-3.7	D;.
REVEL	Uncertain	0.46
Sift	Uncertain	0.0010	D;.
Sift4G	Uncertain	0.042	D;T
Polyphen		0.94	P;.
Vest4		0.60
MutPred		0.79		Gain of methylation at E493 (P = 4e-04);.;
MVP		0.10
MPC		2.4
ClinPred		0.99	D
GERP RS		4.7
Varity_R		0.67
gMVP		0.86

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: chr19-49933982;