rs782192446
Positions:
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001363118.2(SLC52A2):c.185T>A(p.Leu62Gln) variant causes a missense change. The variant allele was found at a frequency of 0.00000684 in 1,461,490 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.0000068 ( 0 hom. )
Consequence
SLC52A2
NM_001363118.2 missense
NM_001363118.2 missense
Scores
2
10
6
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 5.82
Genes affected
SLC52A2 (HGNC:30224): (solute carrier family 52 member 2) This gene encodes a membrane protein which belongs to the riboflavin transporter family. In humans, riboflavin must be obtained by intestinal absorption because it cannot be synthesized by the body. The water-soluble vitamin riboflavin is processed to the coenzymes flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD) which then act as intermediaries in many cellular metabolic reactions. Paralogous members of the riboflavin transporter gene family are located on chromosomes 17 and 20. Unlike other members of this family, this gene has higher expression in brain tissue than small intestine. Alternative splicing of this gene results in multiple transcript variants encoding the same protein. Mutations in this gene have been associated with Brown-Vialetto-Van Laere syndrome 2 - an autosomal recessive progressive neurologic disorder characterized by deafness, bulbar dysfunction, and axial and limb hypotonia. [provided by RefSeq, Jul 2012]
Genome browser will be placed here
ACMG classification
Classification made for transcript
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/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC52A2 | NM_001363118.2 | c.185T>A | p.Leu62Gln | missense_variant | 3/5 | ENST00000643944.2 | NP_001350047.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC52A2 | ENST00000643944.2 | c.185T>A | p.Leu62Gln | missense_variant | 3/5 | NM_001363118.2 | ENSP00000496184.2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
Cov.:
33
GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461490Hom.: 0 Cov.: 30 AF XY: 0.00000825 AC XY: 6AN XY: 727044
GnomAD4 exome
AF:
AC:
10
AN:
1461490
Hom.:
Cov.:
30
AF XY:
AC XY:
6
AN XY:
727044
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome Cov.: 33
GnomAD4 genome
Cov.:
33
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Benign
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Benign
.;T;T;T;T;T;T;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
M_CAP
Pathogenic
D
MetaRNN
Uncertain
D;D;D;D;D;D;D;D
MetaSVM
Benign
T
MutationAssessor
Uncertain
.;M;M;M;.;M;M;M
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N;N;N;N;N;.
REVEL
Uncertain
Sift
Uncertain
D;D;D;D;D;D;D;.
Sift4G
Benign
T;D;D;D;T;D;D;.
Polyphen
0.99
.;D;D;D;.;D;D;D
Vest4
0.69, 0.69
MutPred
Gain of MoRF binding (P = 0.0542);Gain of MoRF binding (P = 0.0542);Gain of MoRF binding (P = 0.0542);Gain of MoRF binding (P = 0.0542);Gain of MoRF binding (P = 0.0542);Gain of MoRF binding (P = 0.0542);Gain of MoRF binding (P = 0.0542);Gain of MoRF binding (P = 0.0542);
MVP
MPC
0.48
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at