rs587777056
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM4PP3PP5
The NM_020988.3(GNAO1):c.572_592del(p.Thr191_Phe197del) variant causes a inframe deletion change involving the alteration of a conserved nucleotide. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Genomes: not found (cov: 35)
Consequence
GNAO1
NM_020988.3 inframe_deletion
NM_020988.3 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 9.27
Genes affected
GNAO1 (HGNC:4389): (G protein subunit alpha o1) The protein encoded by this gene represents the alpha subunit of the Go heterotrimeric G-protein signal-transducing complex. Defects in this gene are a cause of early-onset epileptic encephalopathy. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2015]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 4 ACMG points.
PM4
?
Nonframeshift variant in NON repetitive region in NM_020988.3.
PP3
?
No computational evidence supports a deleterious effect, but strongly conserved according to phyloP
PP5
?
Variant 16-56334827-CCCACTTCACATTCAAGAACCT-C is Pathogenic according to our data. Variant chr16-56334827-CCCACTTCACATTCAAGAACCT-C is described in ClinVar as [Pathogenic]. Clinvar id is 66114.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr16-56334827-CCCACTTCACATTCAAGAACCT-C is described in Lovd as [Pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GNAO1 | NM_020988.3 | c.572_592del | p.Thr191_Phe197del | inframe_deletion | 5/9 | ENST00000262493.12 | |
GNAO1 | NM_138736.3 | c.572_592del | p.Thr191_Phe197del | inframe_deletion | 5/8 | ||
GNAO1 | XM_011523003.4 | c.446_466del | p.Thr149_Phe155del | inframe_deletion | 5/9 | ||
GNAO1 | XR_007064866.1 | n.1319_1339del | non_coding_transcript_exon_variant | 5/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GNAO1 | ENST00000262493.12 | c.572_592del | p.Thr191_Phe197del | inframe_deletion | 5/9 | 1 | NM_020988.3 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 35
GnomAD3 genomes
?
Cov.:
35
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Cov.: 35
GnomAD4 genome
?
Cov.:
35
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Developmental and epileptic encephalopathy, 17 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Sep 05, 2013 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at