chr11-1017463-TTCTG-T
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Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PVS1PM2
The NM_005961.3(MUC6):c.5334_5337del(p.Arg1779ProfsTer69) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000874 in 1,602,688 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: 𝑓 0.000066 ( 0 hom., cov: 118)
Exomes 𝑓: 0.0000028 ( 0 hom. )
Consequence
MUC6
NM_005961.3 frameshift
NM_005961.3 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -2.47
Genes affected
MUC6 (HGNC:7517): (mucin 6, oligomeric mucus/gel-forming) This gene encodes a member of the mucin protein family. Mucins are high molecular weight glycoproteins produced by many epithelial tissues. The protein encoded by this gene is secreted and forms an insoluble mucous barrier that protects the gut lumen. [provided by RefSeq, Dec 2016]
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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 |
|---|---|---|---|---|---|---|---|---|
| MUC6 | NM_005961.3 | c.5334_5337del | p.Arg1779ProfsTer69 | frameshift_variant | 31/33 | ENST00000421673.7 | NP_005952.2 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| MUC6 | ENST00000421673.7 | c.5334_5337del | p.Arg1779ProfsTer69 | frameshift_variant | 31/33 | 5 | NM_005961.3 | ENSP00000406861 | P1 |
Frequencies
GnomAD3 genomes 0.0000660 AC: 10AN: 151500Hom.: 0 Cov.: 118
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GnomAD4 exome AF: 0.00000276 AC: 4AN: 1451070Hom.: 0 AF XY: 0.00000416 AC XY: 3AN XY: 721584
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GnomAD4 genome 0.0000660 AC: 10AN: 151618Hom.: 0 Cov.: 118 AF XY: 0.0000674 AC XY: 5AN XY: 74176
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ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Lung cancer Pathogenic:1
| Pathogenic, no assertion criteria provided | research | Arun Kumar Laboratory, Indian Institute of Science | Jun 15, 2021 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at