X-77969227-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001029891.3(PGAM4):āc.412A>Gā(p.Lys138Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001029891.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PGAM4 | NM_001029891.3 | c.412A>G | p.Lys138Glu | missense_variant | Exon 1 of 1 | ENST00000458128.3 | NP_001025062.1 | |
ATP7A | NM_000052.7 | c.-21-2394T>C | intron_variant | Intron 1 of 22 | ENST00000341514.11 | NP_000043.4 | ||
ATP7A | NM_001282224.2 | c.-21-2394T>C | intron_variant | Intron 1 of 21 | NP_001269153.1 | |||
ATP7A | NR_104109.2 | n.144-2394T>C | intron_variant | Intron 1 of 9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PGAM4 | ENST00000458128.3 | c.412A>G | p.Lys138Glu | missense_variant | Exon 1 of 1 | 6 | NM_001029891.3 | ENSP00000412189.1 | ||
ATP7A | ENST00000341514.11 | c.-21-2394T>C | intron_variant | Intron 1 of 22 | 1 | NM_000052.7 | ENSP00000345728.6 |
Frequencies
GnomAD3 genomes Cov.: 23
GnomAD3 exomes AF: 0.0000165 AC: 3AN: 182309Hom.: 0 AF XY: 0.0000148 AC XY: 1AN XY: 67493
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000182 AC: 2AN: 1098168Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 363580
GnomAD4 genome Cov.: 23
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.412A>G (p.K138E) alteration is located in exon 1 (coding exon 1) of the PGAM4 gene. This alteration results from a A to G substitution at nucleotide position 412, causing the lysine (K) at amino acid position 138 to be replaced by a glutamic acid (E). 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