1-18634363-G-A
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_001135254.2(PAX7):c.146G>A(p.Arg49Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000929 in 1,613,876 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 12/21 in silico tools predict a damaging outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_001135254.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PAX7 | NM_001135254.2 | c.146G>A | p.Arg49Gln | missense_variant | 2/9 | ENST00000420770.7 | NP_001128726.1 | |
PAX7 | NM_002584.3 | c.146G>A | p.Arg49Gln | missense_variant | 2/8 | NP_002575.1 | ||
PAX7 | NM_013945.3 | c.146G>A | p.Arg49Gln | missense_variant | 2/8 | NP_039236.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PAX7 | ENST00000420770.7 | c.146G>A | p.Arg49Gln | missense_variant | 2/9 | 1 | NM_001135254.2 | ENSP00000403389.2 | ||
PAX7 | ENST00000375375.7 | c.146G>A | p.Arg49Gln | missense_variant | 2/8 | 1 | ENSP00000364524.3 | |||
PAX7 | ENST00000400661.3 | c.146G>A | p.Arg49Gln | missense_variant | 2/8 | 1 | ENSP00000383502.3 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152198Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250444Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135578
GnomAD4 exome AF: 0.00000889 AC: 13AN: 1461678Hom.: 0 Cov.: 32 AF XY: 0.00000550 AC XY: 4AN XY: 727138
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152198Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74348
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 14, 2024 | The c.146G>A (p.R49Q) alteration is located in exon 2 (coding exon 2) of the PAX7 gene. This alteration results from a G to A substitution at nucleotide position 146, causing the arginine (R) at amino acid position 49 to be replaced by a glutamine (Q). 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