12-20732953-G-A
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_017435.5(SLCO1C1):c.1231G>A(p.Gly411Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000248 in 1,613,874 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 12/21 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_017435.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLCO1C1 | NM_017435.5 | c.1231G>A | p.Gly411Arg | missense_variant | 10/15 | ENST00000266509.7 | |
SLCO1C1 | NM_001145946.2 | c.1231G>A | p.Gly411Arg | missense_variant | 11/16 | ||
SLCO1C1 | NM_001145945.2 | c.1084G>A | p.Gly362Arg | missense_variant | 10/15 | ||
SLCO1C1 | NM_001145944.2 | c.877G>A | p.Gly293Arg | missense_variant | 8/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLCO1C1 | ENST00000266509.7 | c.1231G>A | p.Gly411Arg | missense_variant | 10/15 | 1 | NM_017435.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152118Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251324Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135846
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461756Hom.: 0 Cov.: 30 AF XY: 0.00000275 AC XY: 2AN XY: 727188
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152118Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74318
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 22, 2023 | The c.1231G>A (p.G411R) alteration is located in exon 11 (coding exon 9) of the SLCO1C1 gene. This alteration results from a G to A substitution at nucleotide position 1231, causing the glycine (G) at amino acid position 411 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at