rs35191146
Positions:
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The ENST00000366963.9(SLC22A1):c.1260del(p.Met420IlefsTer11) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 28)
Consequence
SLC22A1
ENST00000366963.9 frameshift
ENST00000366963.9 frameshift
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.526
Genes affected
SLC22A1 (HGNC:10963): (solute carrier family 22 member 1) Polyspecific organic cation transporters in the liver, kidney, intestine, and other organs are critical for elimination of many endogenous small organic cations as well as a wide array of drugs and environmental toxins. This gene is one of three similar cation transporter genes located in a cluster on chromosome 6. The encoded protein contains twelve putative transmembrane domains and is a plasma integral membrane protein. Two transcript variants encoding two different isoforms have been found for this gene, but only the longer variant encodes a functional transporter. [provided by RefSeq, Jul 2008]
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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 |
---|---|---|---|---|---|---|---|---|
SLC22A1 | NM_003057.3 | c.1260del | p.Met420IlefsTer11 | frameshift_variant | 7/11 | ENST00000366963.9 | NP_003048.1 | |
SLC22A1 | NM_153187.2 | c.1260del | p.Met420IlefsTer11 | frameshift_variant | 7/10 | NP_694857.1 | ||
SLC22A1 | XM_005267103.3 | c.1260del | p.Met420IlefsTer11 | frameshift_variant | 7/12 | XP_005267160.1 | ||
SLC22A1 | XM_006715552.3 | c.1260del | p.Met420IlefsTer11 | frameshift_variant | 7/9 | XP_006715615.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC22A1 | ENST00000366963.9 | c.1260del | p.Met420IlefsTer11 | frameshift_variant | 7/11 | 1 | NM_003057.3 | ENSP00000355930 | P1 |
Frequencies
GnomAD3 genomes Cov.: 28
GnomAD3 genomes
Cov.:
28
GnomAD4 exome Cov.: 31
GnomAD4 exome
Cov.:
31
GnomAD4 genome Cov.: 28
GnomAD4 genome
Cov.:
28
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
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