rs1259089546

Variant names:

• chr12-39951359-G-A
• rs1259089546
• NM_052885.4:c.932C>T

Your query was ambiguous. Multiple possible variants found:

• chr12-39951359-G-A
• chr12-39951359-G-C
• chr12-39951359-G-T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_052885.4(SLC2A13):​c.932C>T​(p.Pro311Leu) variant causes a missense change. The variant allele was found at a frequency of 0.00000213 in 1,409,096 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P311H) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000021 (0 hom.)
• Consequence: SLC2A13 NM_052885.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.95
• Publications: 0 publications found

Genes affected

SLC2A13 (HGNC:15956): (solute carrier family 2 member 13) Enables ATPase binding activity; myo-inositol:proton symporter activity; and protease binding activity. Involved in myo-inositol transport and positive regulation of amyloid-beta formation. Is integral component of plasma membrane. Part of cell body; cell periphery; and cell projection. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.24856326).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC2A13	NM_052885.4	c.932C>T	p.Pro311Leu	missense_variant	Exon 4 of 10	ENST00000280871.9	NP_443117.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC2A13	ENST00000280871.9	c.932C>T	p.Pro311Leu	missense_variant	Exon 4 of 10	1	NM_052885.4	ENSP00000280871.4
SLC2A13	ENST00000380858.1	c.932C>T	p.Pro311Leu	missense_variant	Exon 4 of 4	1		ENSP00000370239.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000213 AC: 3 AN: 1409096 Hom.: 0 Cov.: 30 AF XY: 0.00000429 AC XY: 3 AN XY: 699860

African (AFR) AF: 0.00 AC: 0 AN: 30500

American (AMR) AF: 0.00 AC: 0 AN: 31936

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 23674

East Asian (EAS) AF: 0.00 AC: 0 AN: 38720

South Asian (SAS) AF: 0.0000131 AC: 1 AN: 76322

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 52186

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5496

European-Non Finnish (NFE) AF: 0.00000183 AC: 2 AN: 1092410

Other (OTH) AF: 0.00 AC: 0 AN: 57852

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.093
BayesDel_addAF	Pathogenic	0.29	D
BayesDel_noAF	Pathogenic	0.17
CADD	Benign	22
DANN	Benign	0.90
DEOGEN2	Benign	0.22	T;T
Eigen	Benign	-0.0050
Eigen_PC	Benign	0.20
FATHMM_MKL	Uncertain	0.97	D
LIST_S2	Uncertain	0.90	D;D
M_CAP	Benign	0.025	D
MetaRNN	Benign	0.25	T;T
MetaSVM	Benign	-0.80	T
MutationAssessor	Benign	1.1	L;.
PhyloP100		6.9
PrimateAI	Uncertain	0.74	T
PROVEAN	Uncertain	-2.5	N;N
REVEL	Uncertain	0.35
Sift	Benign	0.25	T;T
Sift4G	Benign	0.18	T;T
Polyphen		0.073	B;B
Vest4		0.64
MutPred		0.53		Loss of disorder (P = 0.049);Loss of disorder (P = 0.049);
MVP		0.80
MPC		0.25
ClinPred		0.76	D
GERP RS		5.2
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.14
gMVP		0.80
Mutation Taster		=34/66	disease causing

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

Other links and lift over

dbSNP: rs1259089546; hg19: chr12-40345161;