chr11-61766173-GCACCGGGCCCCCCATC-T
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1PM2PP5
The NM_001127392.3(MYRF):c.350_366delinsT(p.Gly117ValfsTer31) variant causes a frameshift change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 33)
Consequence
MYRF
NM_001127392.3 frameshift
NM_001127392.3 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 4.58
Genes affected
MYRF (HGNC:1181): (myelin regulatory factor) This gene encodes a transcription factor that is required for central nervous system myelination and may regulate oligodendrocyte differentiation. It is thought to act by increasing the expression of genes that effect myelin production but may also directly promote myelin gene expression. Loss of a similar gene in mouse models results in severe demyelination. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2014]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 11 ACMG points.
PVS1
?
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
?
Very rare variant in population databases, with high coverage;
PP5
?
Variant 11-61766173-GCACCGGGCCCCCCATC-T is Pathogenic according to our data. Variant chr11-61766173-GCACCGGGCCCCCCATC-T is described in ClinVar as [Pathogenic]. Clinvar id is 635276.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYRF | NM_001127392.3 | c.350_366delinsT | p.Gly117ValfsTer31 | frameshift_variant | 3/27 | ENST00000278836.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYRF | ENST00000278836.10 | c.350_366delinsT | p.Gly117ValfsTer31 | frameshift_variant | 3/27 | 1 | NM_001127392.3 | P2 | |
MYRF | ENST00000265460.9 | c.323_339delinsT | p.Gly108ValfsTer31 | frameshift_variant | 3/26 | 1 | A2 | ||
MYRF | ENST00000675319.1 | c.57_73delinsT | p.Gly20ValfsTer36 | frameshift_variant | 1/23 | ||||
MYRF | ENST00000537766.1 | n.698_714delinsT | non_coding_transcript_exon_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 genomes
?
Cov.:
33
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Cov.: 33
GnomAD4 genome
?
Cov.:
33
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Cardiac-urogenital syndrome Pathogenic:1
Pathogenic, no assertion criteria provided | research | Daryl Scott Lab, Baylor College of Medicine | Apr 06, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at