rs1057517684
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 4P and 1B. PM2PP5_ModerateBP4
The NM_207421.4(PADI6):c.1618G>A(p.Gly540Arg) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,458,614 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 9/12 in silico tools predict a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely pathogenic (★).
Frequency
Consequence
NM_207421.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PADI6 | NM_207421.4 | c.1618G>A | p.Gly540Arg | missense_variant, splice_region_variant | 13/16 | ENST00000619609.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PADI6 | ENST00000619609.1 | c.1618G>A | p.Gly540Arg | missense_variant, splice_region_variant | 13/16 | 1 | NM_207421.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000408 AC: 1AN: 244960Hom.: 0 AF XY: 0.00000753 AC XY: 1AN XY: 132860
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1458614Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 725154
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Preimplantation embryonic lethality 2 Pathogenic:2
Pathogenic, no assertion criteria provided | literature only | OMIM | Apr 10, 2023 | - - |
Likely pathogenic, criteria provided, single submitter | case-control | Wang Lab, The Lab for Reproductive Genetics, Fudan University | Nov 01, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at