5-135028784-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_002653.5(PITX1):āc.940A>Gā(p.Ser314Gly) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000132 in 151,638 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_002653.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PITX1 | NM_002653.5 | c.940A>G | p.Ser314Gly | missense_variant | Exon 3 of 3 | ENST00000265340.12 | NP_002644.4 | |
PITX1 | XM_047417318.1 | c.1042A>G | p.Ser348Gly | missense_variant | Exon 4 of 4 | XP_047273274.1 | ||
PITX1 | XM_047417319.1 | c.595A>G | p.Ser199Gly | missense_variant | Exon 3 of 3 | XP_047273275.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151638Hom.: 0 Cov.: 33
GnomAD4 exome Cov.: 31
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151638Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74076
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.940A>G (p.S314G) alteration is located in exon 3 (coding exon 3) of the PITX1 gene. This alteration results from a A to G substitution at nucleotide position 940, causing the serine (S) at amino acid position 314 to be replaced by a glycine (G). 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