rs1556046904
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PVS1_StrongPM2PP5_Moderate
The NM_139058.3(ARX):c.1469_1470insGGCGACAAGCGGCGGGAGACGCTGCCCGAGGCGCCGCGCACAGCTCCCGAGGCCATGACCGCGCTGTTTGCTCTCCCTGCAGGCTCTTTTCCACAATGGCCCC(p.Leu491AlafsTer19) variant causes a stop gained, frameshift change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. P490P) has been classified as Likely benign.
Frequency
Consequence
NM_139058.3 stop_gained, frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARX | NM_139058.3 | c.1469_1470insGGCGACAAGCGGCGGGAGACGCTGCCCGAGGCGCCGCGCACAGCTCCCGAGGCCATGACCGCGCTGTTTGCTCTCCCTGCAGGCTCTTTTCCACAATGGCCCC | p.Leu491AlafsTer19 | stop_gained, frameshift_variant | 5/5 | ENST00000379044.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARX | ENST00000379044.5 | c.1469_1470insGGCGACAAGCGGCGGGAGACGCTGCCCGAGGCGCCGCGCACAGCTCCCGAGGCCATGACCGCGCTGTTTGCTCTCCCTGCAGGCTCTTTTCCACAATGGCCCC | p.Leu491AlafsTer19 | stop_gained, frameshift_variant | 5/5 | 1 | NM_139058.3 | P1 | |
ARX | ENST00000636885.1 | n.57_58insGGCGACAAGCGGCGGGAGACGCTGCCCGAGGCGCCGCGCACAGCTCCCGAGGCCATGACCGCGCTGTTTGCTCTCCCTGCAGGCTCTTTTCCACAATGGCCCC | non_coding_transcript_exon_variant | 2/2 | 5 |
Frequencies
GnomAD3 genomes Cov.: 24
GnomAD4 exome Cov.: 31
GnomAD4 genome Cov.: 24
ClinVar
Submissions by phenotype
X-linked lissencephaly with abnormal genitalia Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Feb 08, 2013 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at