rs370391854
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2BP4
The NM_001280561.2(CATSPERQ):c.98C>T(p.Ala33Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. 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 (no stars).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
CATSPERQ
NM_001280561.2 missense
NM_001280561.2 missense
Scores
3
6
8
Clinical Significance
Conservation
PhyloP100: 3.43
Publications
0 publications found
Genes affected
CATSPERQ (HGNC:44155): (transmembrane protein 249) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]
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]
SLC52A2 Gene-Disease associations (from GenCC):
- Brown-Vialetto-van Laere syndrome 2Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: ClinGen, Genomics England PanelApp, PanelApp Australia, Labcorp Genetics (formerly Invitae), G2P
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.32949153).
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| CATSPERQ | NM_001280561.2 | c.98C>T | p.Ala33Val | missense_variant | Exon 2 of 6 | ENST00000696146.1 | NP_001267490.1 | |
| CATSPERQ | NM_001252402.3 | c.98C>T | p.Ala33Val | missense_variant | Exon 1 of 5 | NP_001239331.1 | ||
| CATSPERQ | NM_001252404.3 | c.98C>T | p.Ala33Val | missense_variant | Exon 1 of 4 | NP_001239333.1 | ||
| CATSPERQ | NR_047684.3 | n.262C>T | non_coding_transcript_exon_variant | Exon 1 of 5 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| TMEM249 | ENST00000696146.1 | c.98C>T | p.Ala33Val | missense_variant | Exon 2 of 6 | NM_001280561.2 | ENSP00000512438.1 | |||
| ENSG00000271698 | ENST00000531225.1 | n.*787C>T | non_coding_transcript_exon_variant | Exon 2 of 6 | 2 | ENSP00000436572.2 | ||||
| ENSG00000271698 | ENST00000531225.1 | n.*787C>T | 3_prime_UTR_variant | Exon 2 of 6 | 2 | ENSP00000436572.2 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1383300Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 682598
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1383300
Hom.:
Cov.:
33
AF XY:
AC XY:
0
AN XY:
682598
African (AFR)
AF:
AC:
0
AN:
31576
American (AMR)
AF:
AC:
0
AN:
35686
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25164
East Asian (EAS)
AF:
AC:
0
AN:
35720
South Asian (SAS)
AF:
AC:
0
AN:
79232
European-Finnish (FIN)
AF:
AC:
0
AN:
33764
Middle Eastern (MID)
AF:
AC:
0
AN:
5692
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1078594
Other (OTH)
AF:
AC:
0
AN:
57872
GnomAD4 genome
GnomAD4 genome
Cov.:
32
Alfa
AF:
Hom.:
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Epidermolysis bullosa simplex with nail dystrophy Uncertain:1
-
Department of Molecular Biology and Genetics, Acibadem University
Significance:Uncertain significance
Review Status:no assertion criteria provided
Collection Method:research
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Uncertain
T
BayesDel_noAF
Benign
DANN
Pathogenic
DEOGEN2
Benign
T;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
M_CAP
Pathogenic
D
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
M;.
PhyloP100
PrimateAI
Uncertain
T
PROVEAN
Benign
N;D
Sift
Benign
T;D
Sift4G
Pathogenic
D;.
Polyphen
D;.
Vest4
MutPred
Loss of helix (P = 0.0558);Loss of helix (P = 0.0558);
MVP
ClinPred
D
GERP RS
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
Publications
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