X-77968939-C-G
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP3BS2
The NM_001029891.3(PGAM4):āc.700G>Cā(p.Gly234Arg) variant causes a missense change. The variant allele was found at a frequency of 0.000029 in 1,208,901 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 14 hemizygotes in GnomAD. In-silico tool predicts a pathogenic 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 Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PGAM4 | NM_001029891.3 | c.700G>C | p.Gly234Arg | missense_variant | Exon 1 of 1 | ENST00000458128.3 | NP_001025062.1 | |
ATP7A | NM_000052.7 | c.-21-2682C>G | intron_variant | Intron 1 of 22 | ENST00000341514.11 | NP_000043.4 | ||
ATP7A | NM_001282224.2 | c.-21-2682C>G | intron_variant | Intron 1 of 21 | NP_001269153.1 | |||
ATP7A | NR_104109.2 | n.144-2682C>G | intron_variant | Intron 1 of 9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PGAM4 | ENST00000458128.3 | c.700G>C | p.Gly234Arg | missense_variant | Exon 1 of 1 | 6 | NM_001029891.3 | ENSP00000412189.1 | ||
ATP7A | ENST00000341514.11 | c.-21-2682C>G | intron_variant | Intron 1 of 22 | 1 | NM_000052.7 | ENSP00000345728.6 |
Frequencies
GnomAD3 genomes AF: 0.0000179 AC: 2AN: 111938Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34092
GnomAD3 exomes AF: 0.0000109 AC: 2AN: 183290Hom.: 0 AF XY: 0.0000147 AC XY: 1AN XY: 67800
GnomAD4 exome AF: 0.0000301 AC: 33AN: 1096963Hom.: 0 Cov.: 32 AF XY: 0.0000386 AC XY: 14AN XY: 363163
GnomAD4 genome AF: 0.0000179 AC: 2AN: 111938Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34092
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.700G>C (p.G234R) alteration is located in exon 1 (coding exon 1) of the PGAM4 gene. This alteration results from a G to C substitution at nucleotide position 700, causing the glycine (G) at amino acid position 234 to be replaced by an arginine (R). 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