3-49422391-CG-CGG
Variant names:
Variant summary
Our verdict is Pathogenic. The variant received 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_000481.4(AMT):c.59dupC(p.Ala21GlyfsTer7) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,620 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. P20P) has been classified as Likely benign.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 6.8e-7 ( 0 hom. )
Consequence
AMT
NM_000481.4 frameshift
NM_000481.4 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.545
Publications
1 publications found
Genes affected
AMT (HGNC:473): (aminomethyltransferase) This gene encodes one of four critical components of the glycine cleavage system. Mutations in this gene have been associated with glycine encephalopathy. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2011]
NICN1 (HGNC:18317): (nicolin 1, tubulin polyglutamylase complex subunit) This protein encoded by this gene localizes to the nucleus and is expressed in numerous tissues including brain, testis, liver, and kidney. This refseq contains genomic sequence in its 3' UTR which is not supported by experimental evidence. Computer predictions indicate that this region of the 3' UTR contains hairpin-forming self-complementary sequence which is possibly excised after transcription. This gene has a pseudogene on chromosome X. [provided by RefSeq, Jul 2008]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Pathogenic. The variant received 12 ACMG points.
PVS1
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant located near the start codon (<100nt), not predicted to undergo nonsense mediated mRNA decay. There are 120 pathogenic variants in the truncated region.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 3-49422391-C-CG is Pathogenic according to our data. Variant chr3-49422391-C-CG is described in CliVar as Pathogenic. Clinvar id is 1453525.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr3-49422391-C-CG is described in CliVar as Pathogenic. Clinvar id is 1453525.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr3-49422391-C-CG is described in CliVar as Pathogenic. Clinvar id is 1453525.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr3-49422391-C-CG is described in CliVar as Pathogenic. Clinvar id is 1453525.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr3-49422391-C-CG is described in CliVar as Pathogenic. Clinvar id is 1453525.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr3-49422391-C-CG is described in CliVar as Pathogenic. Clinvar id is 1453525.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr3-49422391-C-CG is described in CliVar as Pathogenic. Clinvar id is 1453525.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr3-49422391-C-CG is described in CliVar as Pathogenic. Clinvar id is 1453525.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr3-49422391-C-CG is described in CliVar as Pathogenic. Clinvar id is 1453525.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr3-49422391-C-CG is described in CliVar as Pathogenic. Clinvar id is 1453525.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr3-49422391-C-CG is described in CliVar as Pathogenic. Clinvar id is 1453525.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr3-49422391-C-CG is described in CliVar as Pathogenic. Clinvar id is 1453525.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr3-49422391-C-CG is described in CliVar as Pathogenic. Clinvar id is 1453525.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr3-49422391-C-CG is described in CliVar as Pathogenic. Clinvar id is 1453525.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr3-49422391-C-CG is described in CliVar as Pathogenic. Clinvar id is 1453525.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| AMT | ENST00000273588.9 | c.59dupC | p.Ala21GlyfsTer7 | frameshift_variant | Exon 1 of 9 | 1 | NM_000481.4 | ENSP00000273588.3 | ||
| NICN1 | ENST00000273598.8 | c.*2441dupC | 3_prime_UTR_variant | Exon 6 of 6 | 1 | NM_032316.3 | ENSP00000273598.4 | |||
| ENSG00000283189 | ENST00000636166.1 | c.496-820dupC | intron_variant | Intron 4 of 10 | 5 | ENSP00000490106.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461620Hom.: 0 Cov.: 36 AF XY: 0.00 AC XY: 0AN XY: 727112 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
AF:
AC:
1
AN:
1461620
Hom.:
Cov.:
36
AF XY:
AC XY:
0
AN XY:
727112
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
0
AN:
33480
American (AMR)
AF:
AC:
0
AN:
44720
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26134
East Asian (EAS)
AF:
AC:
0
AN:
39700
South Asian (SAS)
AF:
AC:
0
AN:
86250
European-Finnish (FIN)
AF:
AC:
1
AN:
53186
Middle Eastern (MID)
AF:
AC:
0
AN:
5768
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1111986
Other (OTH)
AF:
AC:
0
AN:
60396
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.225
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Glycine encephalopathy Pathogenic:1
Jul 12, 2022
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Pathogenic
Review Status:criteria provided, single submitter
Collection Method:clinical testing
This sequence change creates a premature translational stop signal (p.Ala21Glyfs*7) in the AMT gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in AMT are known to be pathogenic (PMID: 16450403). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with AMT-related conditions. ClinVar contains an entry for this variant (Variation ID: 1453525). For these reasons, this variant has been classified as Pathogenic. -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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