1-35893727-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM1PM2PP5

The NM_012199.5(AGO1):​c.566C>T​(p.Pro189Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,684 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000014 ( 0 hom. )

Consequence

AGO1
NM_012199.5 missense

Scores

6
9
4

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:2U:1

Conservation

PhyloP100: 7.91
Variant links:
Genes affected
AGO1 (HGNC:3262): (argonaute RISC component 1) This gene encodes a member of the argonaute family of proteins, which associate with small RNAs and have important roles in RNA interference (RNAi) and RNA silencing. This protein binds to microRNAs (miRNAs) or small interfering RNAs (siRNAs) and represses translation of mRNAs that are complementary to them. It is also involved in transcriptional gene silencing (TGS) of promoter regions that are complementary to bound short antigene RNAs (agRNAs), as well as in the degradation of miRNA-bound mRNA targets. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. A recent study showed this gene to be an authentic stop codon readthrough target, and that its mRNA could give rise to an additional C-terminally extended isoform by use of an alternative in-frame translation termination codon. [provided by RefSeq, Nov 2015]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 5 ACMG points.

PM1
In a strand (size 2) in uniprot entity AGO1_HUMAN there are 5 pathogenic changes around while only 0 benign (100%) in NM_012199.5
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 1-35893727-C-T is Pathogenic according to our data. Variant chr1-35893727-C-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 547981.We mark this variant Likely_pathogenic, oryginal submissions are: {Uncertain_significance=1, Likely_pathogenic=2}. Variant chr1-35893727-C-T is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
AGO1NM_012199.5 linkc.566C>T p.Pro189Leu missense_variant 5/19 ENST00000373204.6 NP_036331.1 Q9UL18B2RAD8
AGO1NM_001317122.2 linkc.566C>T p.Pro189Leu missense_variant 5/19 NP_001304051.1 Q9UL18A0A6I8PTZ8B2RAD8
AGO1NM_001317123.2 linkc.341C>T p.Pro114Leu missense_variant 5/19 NP_001304052.1 Q9UL18Q5TA58B2RAD8B3KME0
AGO1XM_011541236.3 linkc.566C>T p.Pro189Leu missense_variant 5/19 XP_011539538.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
AGO1ENST00000373204.6 linkc.566C>T p.Pro189Leu missense_variant 5/191 NM_012199.5 ENSP00000362300.4 Q9UL18

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
0.00000137
AC:
2
AN:
1461684
Hom.:
0
Cov.:
32
AF XY:
0.00000138
AC XY:
1
AN XY:
727144
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000180
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32
EpiCase
AF:
0.0000545
EpiControl
AF:
0.00

ClinVar

Significance: Conflicting classifications of pathogenicity
Submissions summary: Pathogenic:2Uncertain:1
Revision: criteria provided, conflicting classifications
LINK: link

Submissions by phenotype

not provided Pathogenic:1Uncertain:1
Likely pathogenic, criteria provided, single submitterclinical testingGeneDxNov 13, 2023Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 34930816, 33144682) -
Uncertain significance, criteria provided, single submitterclinical testingMayo Clinic Laboratories, Mayo ClinicJun 23, 2017- -
Neurodevelopmental disorder with language delay and behavioral abnormalities, with or without seizures Pathogenic:1
Likely pathogenic, criteria provided, single submitterclinical testingInstitute of Human Genetics, University of Leipzig Medical CenterAug 09, 2024Criteria applied: PS2_MOD,PM1,PS4_SUP,PM2_SUP -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.61
BayesDel_addAF
Uncertain
0.047
T
BayesDel_noAF
Benign
-0.17
CADD
Pathogenic
33
DANN
Uncertain
1.0
DEOGEN2
Uncertain
0.56
.;D
Eigen
Pathogenic
0.86
Eigen_PC
Pathogenic
0.85
FATHMM_MKL
Uncertain
0.96
D
LIST_S2
Pathogenic
0.99
D;D
M_CAP
Benign
0.046
D
MetaRNN
Uncertain
0.61
D;D
MetaSVM
Benign
-0.99
T
MutationAssessor
Uncertain
2.8
.;M
PrimateAI
Pathogenic
0.89
D
PROVEAN
Pathogenic
-7.4
D;D
REVEL
Uncertain
0.41
Sift
Uncertain
0.0070
D;D
Sift4G
Uncertain
0.039
D;D
Polyphen
0.95
.;P
Vest4
0.58
MutPred
0.61
.;Loss of disorder (P = 0.0206);
MVP
0.62
MPC
2.8
ClinPred
0.99
D
GERP RS
5.9
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.72
gMVP
0.96

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: rs1553154069; hg19: chr1-36359328; API