NM_206965.2:c.1615C>T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_206965.2(FTCD):c.1615C>T(p.Arg539Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000018 in 1,613,228 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_206965.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FTCD | NM_206965.2 | c.1615C>T | p.Arg539Trp | missense_variant | Exon 14 of 14 | ENST00000397746.8 | NP_996848.1 | |
FTCD | NM_001320412.2 | c.1595C>T | p.Pro532Leu | missense_variant | Exon 14 of 15 | NP_001307341.1 | ||
FTCD | NM_006657.3 | c.1615C>T | p.Arg539Trp | missense_variant | Exon 14 of 15 | NP_006648.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152198Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000242 AC: 6AN: 247798Hom.: 0 AF XY: 0.0000223 AC XY: 3AN XY: 134572
GnomAD4 exome AF: 0.0000185 AC: 27AN: 1461030Hom.: 0 Cov.: 36 AF XY: 0.0000138 AC XY: 10AN XY: 726780
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152198Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74336
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.1615C>T (p.R539W) alteration is located in exon 14 (coding exon 14) of the FTCD gene. This alteration results from a C to T substitution at nucleotide position 1615, causing the arginine (R) at amino acid position 539 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Glutamate formiminotransferase deficiency Uncertain:1
This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 539 of the FTCD protein (p.Arg539Trp). This variant is present in population databases (rs756994444, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with FTCD-related conditions. ClinVar contains an entry for this variant (Variation ID: 958004). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at