4-25662738-A-T

Position:

• chr4-25662738-A-T

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP4

The NM_006424.3(SLC34A2):​c.146A>T​(p.Glu49Val) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: SLC34A2 NM_006424.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 3.97

Genes affected

SLC34A2 (HGNC:11020): (solute carrier family 34 member 2) The protein encoded by this gene is a pH-sensitive sodium-dependent phosphate transporter. Phosphate uptake is increased at lower pH. Defects in this gene are a cause of pulmonary alveolar microlithiasis. Three transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, May 2010]

ACMG classification

Verdict is Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.39145645).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC34A2	NM_006424.3	c.146A>T	p.Glu49Val	missense_variant	3/13	ENST00000382051.8	NP_006415.3
SLC34A2	NM_001177998.2	c.143A>T	p.Glu48Val	missense_variant	3/13		NP_001171469.2
SLC34A2	NM_001177999.2	c.143A>T	p.Glu48Val	missense_variant	3/13		NP_001171470.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC34A2	ENST00000382051.8	c.146A>T	p.Glu49Val	missense_variant	3/13	1	NM_006424.3	ENSP00000371483	P4

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

Inborn genetic diseases Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Jan 30, 2024

The c.146A>T (p.E49V) alteration is located in exon 3 (coding exon 2) of the SLC34A2 gene. This alteration results from a A to T substitution at nucleotide position 146, causing the glutamic acid (E) at amino acid position 49 to be replaced by a valine (V). 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	Benign	0.23
BayesDel_addAF	Benign	-0.00052	T
BayesDel_noAF	Benign	-0.24
CADD	Benign	20
DANN	Uncertain	0.98
DEOGEN2	Benign	0.16	.;.;.;T;.;.
Eigen	Benign	0.16
Eigen_PC	Benign	0.093
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Benign	0.74	.;T;.;T;T;T
M_CAP	Benign	0.076	D
MetaRNN	Benign	0.39	T;T;T;T;T;T
MetaSVM	Benign	-0.76	T
MutationAssessor	Uncertain	2.6	.;.;.;M;.;.
MutationTaster	Benign	1.0	D;D;D
PrimateAI	Benign	0.36	T
PROVEAN	Uncertain	-4.2	.;D;D;D;D;D
REVEL	Benign	0.19
Sift	Uncertain	0.0020	.;D;T;T;T;T
Sift4G	Benign	0.094	.;T;T;T;T;D
Polyphen		0.97	D;.;D;D;D;.
Vest4		0.54, 0.52, 0.53
MutPred		0.33		.;.;.;Gain of glycosylation at Y54 (P = 0.0254);.;Gain of glycosylation at Y54 (P = 0.0254);
MVP		0.67
MPC		0.42
ClinPred		0.95	D
GERP RS		4.3
Varity_R		0.21
gMVP		0.55

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: chr4-25664360;