rs119485089
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PVS1PM2
The NM_022041.4(GAN):c.1447C>T(p.Gln483Ter) variant causes a stop gained change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000558 in 1,613,302 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_022041.4 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GAN | NM_022041.4 | c.1447C>T | p.Gln483Ter | stop_gained | 9/11 | ENST00000648994.2 | |
GAN | NM_001377486.1 | c.808C>T | p.Gln270Ter | stop_gained | 8/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GAN | ENST00000648994.2 | c.1447C>T | p.Gln483Ter | stop_gained | 9/11 | NM_022041.4 | P1 | ||
GAN | ENST00000567335.1 | n.5C>T | non_coding_transcript_exon_variant | 1/2 | 3 | ||||
GAN | ENST00000648349.2 | c.*1155C>T | 3_prime_UTR_variant, NMD_transcript_variant | 8/10 | |||||
GAN | ENST00000650388.1 | c.*804C>T | 3_prime_UTR_variant, NMD_transcript_variant | 7/9 |
Frequencies
GnomAD3 genomes ? AF: 0.00000660 AC: 1AN: 151472Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251492Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135922
GnomAD4 exome AF: 0.00000547 AC: 8AN: 1461830Hom.: 0 Cov.: 32 AF XY: 0.00000275 AC XY: 2AN XY: 727226
GnomAD4 genome ? AF: 0.00000660 AC: 1AN: 151472Hom.: 0 Cov.: 30 AF XY: 0.0000135 AC XY: 1AN XY: 73952
ClinVar
Submissions by phenotype
Giant axonal neuropathy 1 Pathogenic:1Uncertain:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Nov 01, 2000 | - - |
Uncertain significance, no assertion criteria provided | literature only | Inherited Neuropathy Consortium Ii, University Of Miami | Jan 06, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at