rs730882123
Positions:
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PM4_SupportingPP5
The NM_033087.4(ALG2):c.214_224delinsAGTCCCCG(p.Gly72_Leu75delinsSerProArg) variant causes a protein altering change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (no stars). Synonymous variant affecting the same amino acid position (i.e. G72G) has been classified as Likely benign.
Frequency
Genomes: not found (cov: 32)
Consequence
ALG2
NM_033087.4 protein_altering
NM_033087.4 protein_altering
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 6.78
Genes affected
ALG2 (HGNC:23159): (ALG2 alpha-1,3/1,6-mannosyltransferase) This gene encodes a member of the glycosyltransferase 1 family. The encoded protein acts as an alpha 1,3 mannosyltransferase, mannosylating Man(2)GlcNAc(2)-dolichol diphosphate and Man(1)GlcNAc(2)-dolichol diphosphate to form Man(3)GlcNAc(2)-dolichol diphosphate. Defects in this gene have been associated with congenital disorder of glycosylation type Ih (CDG-Ii). Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 4 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
PM4
?
Nonframeshift variant in NON repetitive region in NM_033087.4. Strenght limited to Supporting due to length of the change: 1aa.
PP5
?
Variant 9-99221671-AGCCAGTCCCC-CGGGGACT is Pathogenic according to our data. Variant chr9-99221671-AGCCAGTCCCC-CGGGGACT is described in ClinVar as [Pathogenic]. Clinvar id is 183018.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ALG2 | NM_033087.4 | c.214_224delinsAGTCCCCG | p.Gly72_Leu75delinsSerProArg | protein_altering_variant | 1/2 | ENST00000476832.2 | |
ALG2 | NR_024532.2 | n.262_272delinsAGTCCCCG | non_coding_transcript_exon_variant | 1/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ALG2 | ENST00000476832.2 | c.214_224delinsAGTCCCCG | p.Gly72_Leu75delinsSerProArg | protein_altering_variant | 1/2 | 1 | NM_033087.4 | P1 | |
ALG2 | ENST00000238477.5 | c.214_224delinsAGTCCCCG | p.Gly72_Leu75delinsSerProArg | protein_altering_variant, NMD_transcript_variant | 1/3 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Congenital myasthenic syndrome 14 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Apr 01, 2014 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at