NM_002653.5:c.824G>C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PP3_ModerateBS2
The NM_002653.5(PITX1):āc.824G>Cā(p.Arg275Pro) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000112 in 1,613,640 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_002653.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PITX1 | NM_002653.5 | c.824G>C | p.Arg275Pro | missense_variant | Exon 3 of 3 | ENST00000265340.12 | NP_002644.4 | |
PITX1 | XM_047417318.1 | c.926G>C | p.Arg309Pro | missense_variant | Exon 4 of 4 | XP_047273274.1 | ||
PITX1 | XM_047417319.1 | c.479G>C | p.Arg160Pro | missense_variant | Exon 3 of 3 | XP_047273275.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152180Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.00000800 AC: 2AN: 250102Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135554
GnomAD4 exome AF: 0.0000116 AC: 17AN: 1461460Hom.: 0 Cov.: 34 AF XY: 0.0000138 AC XY: 10AN XY: 727080
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152180Hom.: 0 Cov.: 34 AF XY: 0.0000135 AC XY: 1AN XY: 74338
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at