5-135033815-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_002653.5(PITX1):c.67C>T(p.Pro23Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00000434 in 1,383,888 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_002653.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PITX1 | NM_002653.5 | c.67C>T | p.Pro23Ser | missense_variant | Exon 1 of 3 | ENST00000265340.12 | NP_002644.4 | |
PITX1 | XM_047417318.1 | c.169C>T | p.Pro57Ser | missense_variant | Exon 2 of 4 | XP_047273274.1 | ||
PITX1-AS1 | NR_161235.1 | n.267+275G>A | intron_variant | Intron 1 of 5 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD4 exome AF: 0.00000434 AC: 6AN: 1383888Hom.: 0 Cov.: 31 AF XY: 0.00000729 AC XY: 5AN XY: 685982
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.67C>T (p.P23S) alteration is located in exon 1 (coding exon 1) of the PITX1 gene. This alteration results from a C to T substitution at nucleotide position 67, causing the proline (P) at amino acid position 23 to be replaced by a serine (S). 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
Publications
No publications associated with this variant yet.