rs1060499915
Positions:
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PVS1PM2
The NM_030930.4(UNC93B1):c.890delT(p.Phe297fs) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 34)
Consequence
UNC93B1
NM_030930.4 frameshift
NM_030930.4 frameshift
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 7.30
Genes affected
UNC93B1 (HGNC:13481): (unc-93 homolog B1, TLR signaling regulator) This gene encodes a protein that is involved in innate and adaptive immune response by regulating toll-like receptor signaling. The encoded protein traffics nucleotide sensing toll-like receptors to the endolysosome from the endoplasmic reticulum. Deficiency of the encoded protein has been associated with herpes simplex encephalitis. [provided by RefSeq, Feb 2014]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 10 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;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
UNC93B1 | NM_030930.4 | c.890delT | p.Phe297fs | frameshift_variant | 7/11 | ENST00000227471.7 | NP_112192.2 | |
UNC93B1 | XM_011545290.1 | c.479delT | p.Phe160fs | frameshift_variant | 5/9 | XP_011543592.1 | ||
UNC93B1 | XM_011545291.3 | c.335delT | p.Phe112fs | frameshift_variant | 4/8 | XP_011543593.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
UNC93B1 | ENST00000227471.7 | c.890delT | p.Phe297fs | frameshift_variant | 7/11 | 1 | NM_030930.4 | ENSP00000227471.3 | ||
UNC93B1 | ENST00000533424.6 | n.1384delT | non_coding_transcript_exon_variant | 6/7 | 5 | |||||
UNC93B1 | ENST00000622364.4 | n.888delT | non_coding_transcript_exon_variant | 7/7 | 2 | |||||
UNC93B1 | ENST00000531152.3 | n.*28delT | downstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes Cov.: 34
GnomAD3 genomes
Cov.:
34
GnomAD4 exome Cov.: 32
GnomAD4 exome
Cov.:
32
GnomAD4 genome Cov.: 34
GnomAD4 genome
Cov.:
34
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
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