20-763912-G-T

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3

The NM_033409.4(SLC52A3):​c.659C>A​(p.Pro220His) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as not provided (no stars).

Frequency

Genomes: not found (cov: 33)

Consequence

SLC52A3
NM_033409.4 missense

Scores

3
12
4

Clinical Significance

not provided no classification provided O:1

Conservation

PhyloP100: 4.58
Variant links:
Genes affected
SLC52A3 (HGNC:16187): (solute carrier family 52 member 3) This gene encodes a riboflavin transporter protein that is strongly expressed in the intestine and likely plays a role in intestinal absorption of riboflavin. The protein is predicted to have eleven transmembrane domains and a cell surface localization signal in the C-terminus. Mutations at this locus have been associated with Brown-Vialetto-Van Laere syndrome and Fazio-Londe disease. [provided by RefSeq, Mar 2012]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 3 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.827

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SLC52A3NM_033409.4 linkuse as main transcriptc.659C>A p.Pro220His missense_variant 3/5 ENST00000645534.1 NP_212134.3 Q9NQ40-1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SLC52A3ENST00000645534.1 linkuse as main transcriptc.659C>A p.Pro220His missense_variant 3/5 NM_033409.4 ENSP00000494193.1 Q9NQ40-1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
63
GnomAD4 genome
Cov.:
33

ClinVar

Significance: not provided
Submissions summary: Other:1
Revision: no classification provided
LINK: link

Submissions by phenotype

Brown-Vialetto-van Laere syndrome 1 Other:1
not provided, no classification providedliterature onlyGeneReviews-- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.23
BayesDel_addAF
Pathogenic
0.19
D
BayesDel_noAF
Uncertain
0.030
CADD
Pathogenic
27
DANN
Uncertain
1.0
DEOGEN2
Benign
0.16
T;T;.;T;T
Eigen
Uncertain
0.60
Eigen_PC
Uncertain
0.57
FATHMM_MKL
Pathogenic
0.98
D
LIST_S2
Benign
0.84
.;.;T;.;D
M_CAP
Uncertain
0.11
D
MetaRNN
Pathogenic
0.83
D;D;D;D;D
MetaSVM
Uncertain
-0.13
T
MutationAssessor
Uncertain
2.7
M;M;M;M;M
PrimateAI
Uncertain
0.51
T
PROVEAN
Uncertain
-2.8
.;.;D;N;.
REVEL
Uncertain
0.56
Sift
Uncertain
0.025
.;.;D;D;.
Sift4G
Uncertain
0.025
.;D;D;D;.
Polyphen
1.0
D;D;D;D;D
Vest4
0.74, 0.69
MutPred
0.60
Loss of loop (P = 0.0128);Loss of loop (P = 0.0128);Loss of loop (P = 0.0128);Loss of loop (P = 0.0128);Loss of loop (P = 0.0128);
MVP
0.84
MPC
1.0
ClinPred
0.96
D
GERP RS
5.0
Varity_R
0.18
gMVP
0.52

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs797045194; hg19: chr20-744556; API