rs786204460
Positions:
Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong
The ENST00000352480.10(ASS1):c.1138C>T(p.Gln380Ter) variant causes a stop gained change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 32)
Consequence
ASS1
ENST00000352480.10 stop_gained
ENST00000352480.10 stop_gained
Scores
4
2
1
Clinical Significance
Conservation
PhyloP100: 6.10
Genes affected
ASS1 (HGNC:758): (argininosuccinate synthase 1) The protein encoded by this gene catalyzes the penultimate step of the arginine biosynthetic pathway. There are approximately 10 to 14 copies of this gene including the pseudogenes scattered across the human genome, among which the one located on chromosome 9 appears to be the only functional gene for argininosuccinate synthetase. Mutations in the chromosome 9 copy of this gene cause citrullinemia. Two transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Aug 2012]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 18 ACMG points.
PVS1
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 9-130499515-C-T is Pathogenic according to our data. Variant chr9-130499515-C-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 188776.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-130499515-C-T is described in Lovd as [Pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ASS1 | NM_054012.4 | c.1138C>T | p.Gln380Ter | stop_gained | 14/15 | ENST00000352480.10 | NP_446464.1 | |
ASS1 | NM_000050.4 | c.1138C>T | p.Gln380Ter | stop_gained | 15/16 | NP_000041.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ASS1 | ENST00000352480.10 | c.1138C>T | p.Gln380Ter | stop_gained | 14/15 | 1 | NM_054012.4 | ENSP00000253004 | P1 | |
ASS1 | ENST00000372393.7 | c.1138C>T | p.Gln380Ter | stop_gained | 15/16 | 5 | ENSP00000361469 | P1 | ||
ASS1 | ENST00000372394.5 | c.1138C>T | p.Gln380Ter | stop_gained | 15/16 | 2 | ENSP00000361471 | P1 | ||
ASS1 | ENST00000372386.6 | n.409C>T | non_coding_transcript_exon_variant | 5/6 | 3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Cov.: 31
GnomAD4 exome
Cov.:
31
GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Pathogenic/Likely pathogenic
Submissions summary: Pathogenic:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Citrullinemia Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Sep 18, 2021 | For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 188776). This premature translational stop signal has been observed in individual(s) with citrullinemia (PMID: 12815590). This variant is not present in population databases (ExAC no frequency). This sequence change creates a premature translational stop signal (p.Gln380*) in the ASS1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in ASS1 are known to be pathogenic (PMID: 18473344, 19006241). - |
Citrullinemia type I Pathogenic:1
Likely pathogenic, criteria provided, single submitter | literature only | Counsyl | May 08, 2014 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Uncertain
Eigen
Pathogenic
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
MutationTaster
Benign
A;A;A;A
Vest4
GERP RS
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