chr10-89593862-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_148977.3(PANK1):c.1027G>A(p.Gly343Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000411 in 1,461,614 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 13/21 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_148977.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PANK1 | ENST00000307534.10 | c.1027G>A | p.Gly343Arg | missense_variant | Exon 4 of 7 | 1 | NM_148977.3 | ENSP00000302108.5 | ||
PANK1 | ENST00000342512.4 | c.763G>A | p.Gly255Arg | missense_variant | Exon 4 of 7 | 1 | ENSP00000345118.3 | |||
PANK1 | ENST00000322191.10 | c.636-542G>A | intron_variant | Intron 3 of 5 | 1 | ENSP00000318526.6 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000411 AC: 6AN: 1461614Hom.: 0 Cov.: 30 AF XY: 0.00000550 AC XY: 4AN XY: 727136
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not provided Uncertain:1
PANK1: PM2, PP3 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.