NM_018834.6:c.-139G>A
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_018834.6(MATR3):c.-139G>A variant causes a 5 prime UTR change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
MATR3
NM_018834.6 5_prime_UTR
NM_018834.6 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 5.14
Publications
0 publications found
Genes affected
MATR3 (HGNC:6912): (matrin 3) This gene encodes a nuclear matrix protein, which is proposed to stabilize certain messenger RNA species. Mutations of this gene are associated with distal myopathy 2, which often includes vocal cord and pharyngeal weakness. Alternatively spliced transcript variants, including read-through transcripts composed of the upstream small nucleolar RNA host gene 4 (non-protein coding) and matrin 3 gene sequence, have been identified. Pseudogenes of this gene are located on chromosomes 1 and X. [provided by RefSeq, Aug 2013]
MATR3 Gene-Disease associations (from GenCC):
- distal myopathy with vocal cord weaknessInheritance: AD Classification: DEFINITIVE, SUPPORTIVE Submitted by: Orphanet, ClinGen
- amyotrophic lateral sclerosis type 21Inheritance: AD Classification: STRONG, MODERATE Submitted by: Labcorp Genetics (formerly Invitae), Genomics England PanelApp, Ambry Genetics
- amyotrophic lateral sclerosisInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.44).
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_018834.6. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| MATR3 | TSL:1 MANE Select | c.-139G>A | 5_prime_UTR | Exon 2 of 15 | ENSP00000378284.3 | P43243-1 | |||
| MATR3 | TSL:2 | c.-139G>A | 5_prime_UTR | Exon 7 of 20 | ENSP00000422319.1 | A8MXP9 | |||
| MATR3 | TSL:1 | c.-139G>A | 5_prime_UTR | Exon 2 of 15 | ENSP00000482895.1 | P43243-1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 1268670Hom.: 0 Cov.: 28 AF XY: 0.00 AC XY: 0AN XY: 617268
GnomAD4 exome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
AC:
0
AN:
1268670
Hom.:
Cov.:
28
AF XY:
AC XY:
0
AN XY:
617268
African (AFR)
AF:
AC:
0
AN:
27696
American (AMR)
AF:
AC:
0
AN:
18010
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
18734
East Asian (EAS)
AF:
AC:
0
AN:
33836
South Asian (SAS)
AF:
AC:
0
AN:
54140
European-Finnish (FIN)
AF:
AC:
0
AN:
31320
Middle Eastern (MID)
AF:
AC:
0
AN:
3554
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1028642
Other (OTH)
AF:
AC:
0
AN:
52738
GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
ClinVar submissions
View on ClinVar Significance:Uncertain significance
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
1
-
Amyotrophic lateral sclerosis type 21 (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
RBP_binding_hub_radar
RBP_regulation_power_radar
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
Publications
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.