16-81365064-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_022041.4(GAN):c.1327C>T(p.Pro443Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00000205 in 1,461,542 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P443A) has been classified as Uncertain significance.
Frequency
Consequence
NM_022041.4 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 | UniProt |
---|---|---|---|---|---|---|---|
GAN | NM_022041.4 | c.1327C>T | p.Pro443Ser | missense_variant | 8/11 | ENST00000648994.2 | |
GAN | NM_001377486.1 | c.688C>T | p.Pro230Ser | missense_variant | 7/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GAN | ENST00000648994.2 | c.1327C>T | p.Pro443Ser | missense_variant | 8/11 | NM_022041.4 | P1 | ||
GAN | ENST00000648349.2 | c.*1035C>T | 3_prime_UTR_variant, NMD_transcript_variant | 7/10 | |||||
GAN | ENST00000650388.1 | c.*684C>T | 3_prime_UTR_variant, NMD_transcript_variant | 6/9 |
Frequencies
GnomAD3 genomes Cov.: 30
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251440Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135898
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461542Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 727110
GnomAD4 genome Cov.: 30
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at