5-177385787-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_003052.5(SLC34A1):​c.46C>T​(p.Leu16Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000821 in 1,461,072 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 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)
Exomes 𝑓: 0.0000082 ( 0 hom. )

Consequence

SLC34A1
NM_003052.5 missense

Scores

2
17

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 1.29
Variant links:
Genes affected
SLC34A1 (HGNC:11019): (solute carrier family 34 member 1) Enables sodium:phosphate symporter activity. Involved in several processes, including phosphate ion homeostasis; phosphate ion transport; and response to lead ion. Located in several cellular components, including apical plasma membrane; mitotic spindle; and nuclear speck. Implicated in several diseases, including Fanconi syndrome (multiple); chronic kidney disease; hereditary hypophosphatemic rickets with hypercalciuria; hypophosphatemic nephrolithiasis/osteoporosis 1; and nephrolithiasis. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

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=0.14087293).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SLC34A1NM_003052.5 linkuse as main transcriptc.46C>T p.Leu16Phe missense_variant 2/13 ENST00000324417.6 NP_003043.3 Q06495-1A0A024R7R9Q86VN6Q7Z725
SLC34A1NM_001167579.2 linkuse as main transcriptc.46C>T p.Leu16Phe missense_variant 2/9 NP_001161051.1 Q06495-2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SLC34A1ENST00000324417.6 linkuse as main transcriptc.46C>T p.Leu16Phe missense_variant 2/131 NM_003052.5 ENSP00000321424.4 Q06495-1
SLC34A1ENST00000512593.5 linkuse as main transcriptc.46C>T p.Leu16Phe missense_variant 2/92 ENSP00000423022.1 Q06495-2
SLC34A1ENST00000504577.5 linkuse as main transcriptc.46C>T p.Leu16Phe missense_variant 2/44 ENSP00000423733.1 D6RCE5
SLC34A1ENST00000507685.5 linkuse as main transcriptn.130C>T non_coding_transcript_exon_variant 2/102

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD3 exomes
AF:
0.0000122
AC:
3
AN:
246456
Hom.:
0
AF XY:
0.0000150
AC XY:
2
AN XY:
133452
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000330
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000181
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000821
AC:
12
AN:
1461072
Hom.:
0
Cov.:
32
AF XY:
0.0000110
AC XY:
8
AN XY:
726776
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000116
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000989
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32
ExAC
AF:
0.00000824
AC:
1

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpMar 29, 2022Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. This variant has not been reported in the literature in individuals affected with SLC34A1-related conditions. This variant is present in population databases (rs762446018, gnomAD 0.003%). This sequence change replaces leucine, which is neutral and non-polar, with phenylalanine, which is neutral and non-polar, at codon 16 of the SLC34A1 protein (p.Leu16Phe). -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.065
BayesDel_addAF
Benign
-0.25
T
BayesDel_noAF
Benign
-0.49
CADD
Benign
18
DANN
Uncertain
0.98
DEOGEN2
Benign
0.15
.;.;T
Eigen
Benign
-0.39
Eigen_PC
Benign
-0.29
FATHMM_MKL
Benign
0.69
D
LIST_S2
Benign
0.74
T;T;T
M_CAP
Benign
0.046
D
MetaRNN
Benign
0.14
T;T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
0.97
.;L;L
PrimateAI
Benign
0.41
T
PROVEAN
Uncertain
-3.4
D;N;N
REVEL
Benign
0.029
Sift
Benign
0.047
D;D;D
Sift4G
Benign
0.27
T;T;T
Polyphen
0.26
.;.;B
Vest4
0.33, 0.25
MutPred
0.18
Gain of methylation at R19 (P = 0.0991);Gain of methylation at R19 (P = 0.0991);Gain of methylation at R19 (P = 0.0991);
MVP
0.46
MPC
0.093
ClinPred
0.082
T
GERP RS
4.0
Varity_R
0.062
gMVP
0.31

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.030
Details are displayed if max score is > 0.2

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: rs762446018; hg19: chr5-176812788; API