NM_033261.3:c.599T>C
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_033261.3(IDI2):āc.599T>Cā(p.Ile200Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000136 in 1,613,992 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 (ā ).
Frequency
Consequence
NM_033261.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IDI2 | NM_033261.3 | c.599T>C | p.Ile200Thr | missense_variant | Exon 5 of 5 | ENST00000277517.2 | NP_150286.1 | |
GTPBP4 | NM_012341.3 | c.*2375A>G | 3_prime_UTR_variant | Exon 17 of 17 | ENST00000360803.9 | NP_036473.2 | ||
GTPBP4 | XM_047424932.1 | c.*2375A>G | 3_prime_UTR_variant | Exon 17 of 17 | XP_047280888.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IDI2 | ENST00000277517.2 | c.599T>C | p.Ile200Thr | missense_variant | Exon 5 of 5 | 1 | NM_033261.3 | ENSP00000277517.1 | ||
GTPBP4 | ENST00000360803.9 | c.*2375A>G | 3_prime_UTR_variant | Exon 17 of 17 | 1 | NM_012341.3 | ENSP00000354040.4 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 151984Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000597 AC: 15AN: 251392Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135870
GnomAD4 exome AF: 0.0000130 AC: 19AN: 1461890Hom.: 0 Cov.: 32 AF XY: 0.0000110 AC XY: 8AN XY: 727246
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152102Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74338
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.599T>C (p.I200T) alteration is located in exon 5 (coding exon 4) of the IDI2 gene. This alteration results from a T to C substitution at nucleotide position 599, causing the isoleucine (I) at amino acid position 200 to be replaced by a threonine (T). 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