rs1554660095
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Uncertain significance. The variant received 1 ACMG points: 1P and 0B. PM4_Supporting
The NM_001128227.3(GNE):c.1133_1135delTGC(p.Leu378del) variant causes a disruptive inframe deletion change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000412 in 1,456,892 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. L378L) has been classified as Likely benign.
Frequency
Genomes: not found (cov: 31)
Exomes 𝑓: 0.0000041 ( 0 hom. )
Consequence
GNE
NM_001128227.3 disruptive_inframe_deletion
NM_001128227.3 disruptive_inframe_deletion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 8.36
Publications
0 publications found
Genes affected
GNE (HGNC:23657): (glucosamine (UDP-N-acetyl)-2-epimerase/N-acetylmannosamine kinase) The protein encoded by this gene is a bifunctional enzyme that initiates and regulates the biosynthesis of N-acetylneuraminic acid (NeuAc), a precursor of sialic acids. It is a rate-limiting enzyme in the sialic acid biosynthetic pathway. Sialic acid modification of cell surface molecules is crucial for their function in many biologic processes, including cell adhesion and signal transduction. Differential sialylation of cell surface molecules is also implicated in the tumorigenicity and metastatic behavior of malignant cells. Mutations in this gene are associated with sialuria, autosomal recessive inclusion body myopathy, and Nonaka myopathy. Alternative splicing of this gene results in transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]
CLTA (HGNC:2090): (clathrin light chain A) Clathrin is a large, soluble protein composed of heavy and light chains. It functions as the main structural component of the lattice-type cytoplasmic face of coated pits and vesicles which entrap specific macromolecules during receptor-mediated endocytosis. This gene encodes one of two clathrin light chain proteins which are believed to function as regulatory elements. Alternative splicing results in multiple transcript variants. Related pseudogenes have been identified on chromosomes 8 and 12. [provided by RefSeq, May 2010]
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 1 ACMG points.
PM4
Nonframeshift variant in NON repetitive region in NM_001128227.3. Strenght limited to Supporting due to length of the change: 1aa.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| GNE | NM_001128227.3 | c.1133_1135delTGC | p.Leu378del | disruptive_inframe_deletion | Exon 6 of 12 | ENST00000396594.8 | NP_001121699.1 | |
| GNE | NM_005476.7 | c.1040_1042delTGC | p.Leu347del | disruptive_inframe_deletion | Exon 6 of 12 | ENST00000642385.2 | NP_005467.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| GNE | ENST00000396594.8 | c.1133_1135delTGC | p.Leu378del | disruptive_inframe_deletion | Exon 6 of 12 | 1 | NM_001128227.3 | ENSP00000379839.3 | ||
| GNE | ENST00000642385.2 | c.1040_1042delTGC | p.Leu347del | disruptive_inframe_deletion | Exon 6 of 12 | NM_005476.7 | ENSP00000494141.2 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
31
GnomAD4 exome AF: 0.00000412 AC: 6AN: 1456892Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 725196 show subpopulations
GnomAD4 exome
AF:
AC:
6
AN:
1456892
Hom.:
AF XY:
AC XY:
0
AN XY:
725196
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33388
American (AMR)
AF:
AC:
0
AN:
44724
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26074
East Asian (EAS)
AF:
AC:
0
AN:
39672
South Asian (SAS)
AF:
AC:
0
AN:
86152
European-Finnish (FIN)
AF:
AC:
0
AN:
53418
Middle Eastern (MID)
AF:
AC:
0
AN:
5758
European-Non Finnish (NFE)
AF:
AC:
6
AN:
1107524
Other (OTH)
AF:
AC:
0
AN:
60182
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.467
Heterozygous variant carriers
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Allele balance
Age Distribution
Exome Het
Variant carriers
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Age
GnomAD4 genome
GnomAD4 genome
Cov.:
31
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
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
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