rs1135401813
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_001371986.1(UNC80):c.2399del(p.Leu800TrpfsTer19) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 33)
Consequence
UNC80
NM_001371986.1 frameshift
NM_001371986.1 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.0290
Genes affected
UNC80 (HGNC:26582): (unc-80 homolog, NALCN channel complex subunit) The protein encoded by this gene is a component of a voltage-independent 'leak' ion-channel complex, in which it performs essential functions, such as serving as a bridge between two other components (sodium leak channel non-selective and UNC79) and as a scaffold for Src kinases. Leak channels play an importnat role in establishment and maintenance of resting membrane potentials in neurons. Mutations in this gene are associated with congenital infantile encephalopathy, intellectual disability and growth issues. [provided by RefSeq, Aug 2016]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 12 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 2-209825971-CT-C is Pathogenic according to our data. Variant chr2-209825971-CT-C is described in ClinVar as [Pathogenic]. Clinvar id is 431143.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UNC80 | NM_001371986.1 | c.2399del | p.Leu800TrpfsTer19 | frameshift_variant | 14/65 | ENST00000673920.1 | |
UNC80 | NM_032504.2 | c.2399del | p.Leu800TrpfsTer19 | frameshift_variant | 14/64 | ||
UNC80 | NM_182587.4 | c.2399del | p.Leu800TrpfsTer19 | frameshift_variant | 14/63 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UNC80 | ENST00000673920.1 | c.2399del | p.Leu800TrpfsTer19 | frameshift_variant | 14/65 | NM_001371986.1 | A2 | ||
UNC80 | ENST00000439458.5 | c.2399del | p.Leu800TrpfsTer19 | frameshift_variant | 14/64 | 5 | P4 | ||
UNC80 | ENST00000673951.1 | c.2399del | p.Leu800TrpfsTer19 | frameshift_variant | 14/64 | A1 | |||
UNC80 | ENST00000272845.10 | c.2399del | p.Leu800TrpfsTer19 | frameshift_variant | 14/63 | 5 | A2 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 genomes
?
Cov.:
33
GnomAD4 exome Cov.: 30
GnomAD4 exome
Cov.:
30
GnomAD4 genome ? Cov.: 33
GnomAD4 genome
?
Cov.:
33
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:2
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Hypotonia, infantile, with psychomotor retardation and characteristic facies 2 Pathogenic:2
Pathogenic, no assertion criteria provided | literature only | Yale Center for Mendelian Genomics, Yale University | Aug 23, 2018 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Groupe Hospitalier Pitie Salpetriere, UF Genomique du Developpement, Assistance Publique Hopitaux de Paris | Jan 06, 2017 | neonatal hypotonia; Intellectual disability, severe; dystonia; unintentional movements of upper limbs; normal CPK and lactates levels - |
Computational scores
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Calibrated prediction
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Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at