5-102249744-C-A
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_180991.5(SLCO4C1):c.1514G>T(p.Cys505Phe) variant causes a missense change. The variant allele was found at a frequency of 0.0000335 in 1,613,774 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_180991.5 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLCO4C1 | NM_180991.5 | c.1514G>T | p.Cys505Phe | missense_variant | Exon 9 of 13 | ENST00000310954.7 | NP_851322.3 | |
SLCO4C1 | XM_011543370.3 | c.1250G>T | p.Cys417Phe | missense_variant | Exon 8 of 12 | XP_011541672.1 | ||
SLCO4C1 | XM_011543372.2 | c.1100G>T | p.Cys367Phe | missense_variant | Exon 11 of 15 | XP_011541674.1 | ||
SLCO4C1 | XM_047417146.1 | c.1100G>T | p.Cys367Phe | missense_variant | Exon 11 of 15 | XP_047273102.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152128Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000399 AC: 10AN: 250828Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135550
GnomAD4 exome AF: 0.0000356 AC: 52AN: 1461646Hom.: 0 Cov.: 31 AF XY: 0.0000426 AC XY: 31AN XY: 727120
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152128Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74308
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1514G>T (p.C505F) alteration is located in exon 9 (coding exon 9) of the SLCO4C1 gene. This alteration results from a G to T substitution at nucleotide position 1514, causing the cysteine (C) at amino acid position 505 to be replaced by a phenylalanine (F). 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