rs1555144358
Positions:
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM1PM2PP3PP5_Moderate
The NM_001940.4(ATN1):c.3172C>T(p.His1058Tyr) variant causes a missense 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 Pathogenic (★).
Frequency
Genomes: not found (cov: 33)
Consequence
ATN1
NM_001940.4 missense
NM_001940.4 missense
Scores
8
8
3
Clinical Significance
Conservation
PhyloP100: 5.87
Genes affected
ATN1 (HGNC:3033): (atrophin 1) Dentatorubral pallidoluysian atrophy (DRPLA) is a rare neurodegenerative disorder characterized by cerebellar ataxia, myoclonic epilepsy, choreoathetosis, and dementia. The disorder is related to the expansion from 7-35 copies to 49-93 copies of a trinucleotide repeat (CAG/CAA) within this gene. The encoded protein includes a serine repeat and a region of alternating acidic and basic amino acids, as well as the variable glutamine repeat. Alternative splicing results in two transcripts variants that encode the same protein. [provided by RefSeq, Jul 2016]
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ACMG classification
Classification made for transcript
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
PM1
In a hotspot region, there are 6 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 4 uncertain in NM_001940.4
PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.828
PP5
Variant 12-6939135-C-T is Pathogenic according to our data. Variant chr12-6939135-C-T is described in ClinVar as [Pathogenic]. Clinvar id is 487497.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-6939135-C-T is described in Lovd as [Pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATN1 | NM_001940.4 | c.3172C>T | p.His1058Tyr | missense_variant | 7/10 | ENST00000396684.3 | |
ATN1 | NM_001007026.2 | c.3172C>T | p.His1058Tyr | missense_variant | 7/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATN1 | ENST00000396684.3 | c.3172C>T | p.His1058Tyr | missense_variant | 7/10 | 1 | NM_001940.4 | P1 | |
ATN1 | ENST00000356654.8 | c.3172C>T | p.His1058Tyr | missense_variant | 7/10 | 1 | P1 | ||
ATN1 | ENST00000537488.1 | n.29C>T | non_coding_transcript_exon_variant | 1/3 | 2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
Cov.:
33
GnomAD4 exome Cov.: 33
GnomAD4 exome
Cov.:
33
GnomAD4 genome Cov.: 33
GnomAD4 genome
Cov.:
33
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:3
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Congenital ATN1 related disorder Pathogenic:1
Pathogenic, no assertion criteria provided | clinical testing | Sydney Children's Hospital, SCHN | Jan 04, 2018 | affected individual has clinical features consistent with congenital ATN1 related disorder - |
Congenital hypotonia, epilepsy, developmental delay, and digital anomalies Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jul 12, 2019 | - - |
ATN1-related disorder Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego | - | This variant has been previously reported as a de novo heterozygous change in a patient with congenital hypotonia, abnormal EEG, developmental delay, and polymicrogyria on brain MRI (PMID: 30827498). The c.3172C>T (p.His1058Tyr) variant is located in the HX Repeat Motif of the ATN1 gene, which is a mutational hotspot for pathogenic variations associated with neurodevelopmental phenotypes (PMID: 30827498). The c.3172C>T (p.His1058Tyr) variant is absent from the gnomAD population database and thus is presumed to be rare. The c.3172C>T (p.His1058Tyr) variant affects a highly conserved amino acid and is predicted by multiple in silico tools to have a deleterious effect on protein function. Analysis of the parental samples was negative for the variant, indicating this variant likely occurred as a de novo event. Based on the available evidence, the c.3172C>T (p.His1058Tyr) variant is classified as Pathogenic. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Pathogenic
D;D
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
.;D
M_CAP
Uncertain
D
MetaRNN
Pathogenic
D;D
MetaSVM
Uncertain
T
MutationAssessor
Uncertain
M;M
MutationTaster
Benign
D;D;D
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D;D
REVEL
Pathogenic
Sift
Pathogenic
D;D
Sift4G
Uncertain
D;D
Polyphen
B;B
Vest4
MutPred
Gain of catalytic residue at Q1053 (P = 8e-04);Gain of catalytic residue at Q1053 (P = 8e-04);
MVP
MPC
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
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