ENST00000262494.13:c.951A>T

Variant summary

Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM2PP2PP3_Moderate

The ENST00000262494.13(GNAO1):​c.951A>T​(p.Lys317Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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. K317R) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 28)

Consequence

GNAO1
ENST00000262494.13 missense

Scores

6
8
2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.93
Variant links:
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 5 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PP2
Missense variant in the GNAO1 gene, where missense mutations are typically associated with disease (based on misZ statistic). The gene has 70 curated pathogenic missense variants (we use a threshold of 10). The gene has 43 curated benign missense variants. Gene score misZ: 3.1919 (above the threshold of 3.09). Trascript score misZ: 3.4487 (above the threshold of 3.09). GenCC associations: The gene is linked to developmental and epileptic encephalopathy, 17, neurodevelopmental disorder with involuntary movements, developmental and epileptic encephalopathy, movement disorder.
PP3
MetaRNN computational evidence supports a deleterious effect, 0.927

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
GNAO1NM_020988.3 linkc.723+6976A>T intron_variant Intron 6 of 8 ENST00000262493.12 NP_066268.1 P09471-1Q8N6I9B3KP89
GNAO1NM_138736.3 linkc.951A>T p.Lys317Asn missense_variant Exon 8 of 8 NP_620073.2 P09471-2Q8N6I9B3KP89Q6AWC5
GNAO1XM_011523003.4 linkc.597+6976A>T intron_variant Intron 6 of 8 XP_011521305.1
GNAO1XR_007064866.1 linkn.1698A>T non_coding_transcript_exon_variant Exon 8 of 9

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
GNAO1ENST00000262493.12 linkc.723+6976A>T intron_variant Intron 6 of 8 1 NM_020988.3 ENSP00000262493.6 P09471-1

Frequencies

GnomAD3 genomes
Cov.:
28
GnomAD4 exome
Cov.:
34
GnomAD4 genome
Cov.:
28

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Uncertain
0.072
D
BayesDel_noAF
Benign
-0.13
CADD
Benign
18
DANN
Uncertain
1.0
Eigen
Uncertain
0.53
Eigen_PC
Uncertain
0.41
FATHMM_MKL
Uncertain
0.78
D
LIST_S2
Pathogenic
0.98
D
M_CAP
Pathogenic
0.68
D
MetaRNN
Pathogenic
0.93
D
MetaSVM
Pathogenic
0.98
D
PrimateAI
Uncertain
0.65
T
PROVEAN
Uncertain
-4.3
D
REVEL
Pathogenic
0.74
Sift
Pathogenic
0.0
D
Sift4G
Uncertain
0.012
D
Polyphen
1.0
D
Vest4
0.76
MutPred
0.61
Loss of methylation at K317 (P = 0.0011);
MVP
0.71
MPC
1.1
ClinPred
0.99
D
GERP RS
4.4
gMVP
0.85

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1799917; hg19: chr16-56377748; API