chr12-6837989-G-A
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_014262.5(P3H3):c.1861G>A(p.Gly621Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000343 in 1,456,600 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 (★).
Frequency
Consequence
NM_014262.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
P3H3 | NM_014262.5 | c.1861G>A | p.Gly621Ser | missense_variant | 13/15 | ENST00000290510.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
P3H3 | ENST00000290510.10 | c.1861G>A | p.Gly621Ser | missense_variant | 13/15 | 1 | NM_014262.5 | P1 | |
P3H3 | ENST00000612048.4 | n.1394G>A | non_coding_transcript_exon_variant | 12/14 | 1 | ||||
P3H3 | ENST00000536140.5 | n.2491G>A | non_coding_transcript_exon_variant | 14/16 | 2 | ||||
P3H3 | ENST00000544200.5 | n.900G>A | non_coding_transcript_exon_variant | 8/8 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome AF: 0.00000343 AC: 5AN: 1456600Hom.: 0 Cov.: 33 AF XY: 0.00000138 AC XY: 1AN XY: 723982
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 21, 2023 | The c.1861G>A (p.G621S) alteration is located in exon 13 (coding exon 13) of the P3H3 gene. This alteration results from a G to A substitution at nucleotide position 1861, causing the glycine (G) at amino acid position 621 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.