chr9-36229049-GCAG-T

Variant names:

• chr9-36229049-GCAG-T
• rs1554660095
• NM_001128227.3:c.1132_1135delCTGCinsA

Variant summary

Our verdict is Uncertain significance. The variant received 5 ACMG points: 5P and 0B. PM2 PM4_Supporting PP2 PP3

The NM_001128227.3(GNE):​c.1132_1135delCTGCinsA​(p.Leu378_His379delinsAsn) variant causes a missense, conservative inframe deletion change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. L378L) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 31)
• Consequence: GNE NM_001128227.3 missense, conservative_inframe_deletion
• Clinical Significance: Uncertain significance criteria provided, single submitter U:2
• 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]

ACMG classification

Our verdict: Uncertain_significance. The variant received 5 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PM4: Nonframeshift variant in NON repetitive region in NM_001128227.3. Strenght limited to Supporting due to length of the change: 1aa.
• PP2: Missense variant in the GNE gene, where missense mutations are typically associated with disease (based on misZ statistic). The gene has 44 curated pathogenic missense variants (we use a threshold of 10). The gene has 1 curated benign missense variants. Gene score misZ: 2.5904 (below the threshold of 3.09). Trascript score misZ: 4.032 (above the threshold of 3.09). GenCC associations: The gene is linked to sialuria, GNE myopathy, congenital myopathy, platelet-type bleeding disorder 19, macrothrombocytopenia, isolated.
• PP3: No computational evidence supports a deleterious effect, but strongly conserved according to phyloP

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001128227.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GNE	NM_001128227.3	MANE Plus Clinical	c.1132_1135delCTGCinsA	p.Leu378_His379delinsAsn	missense conservative_inframe_deletion	Exon 6 of 12	NP_001121699.1
	GNE	NM_005476.7	MANE Select	c.1039_1042delCTGCinsA	p.Leu347_His348delinsAsn	missense conservative_inframe_deletion	Exon 6 of 12	NP_005467.1
	GNE	NM_001374797.1		c.886_889delCTGCinsA	p.Leu296_His297delinsAsn	missense conservative_inframe_deletion	Exon 5 of 11	NP_001361726.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GNE	ENST00000396594.8	TSL:1 MANE Plus Clinical	c.1132_1135delCTGCinsA	p.Leu378_His379delinsAsn	missense conservative_inframe_deletion	Exon 6 of 12	ENSP00000379839.3
	GNE	ENST00000642385.2	MANE Select	c.1039_1042delCTGCinsA	p.Leu347_His348delinsAsn	missense conservative_inframe_deletion	Exon 6 of 12	ENSP00000494141.2
	GNE	ENST00000543356.7	TSL:1	c.862_865delCTGCinsA	p.Leu288_His289delinsAsn	missense conservative_inframe_deletion	Exon 5 of 11	ENSP00000437765.3

Frequencies

GnomAD3 genomes Cov.: 31

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 31

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:2

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Mar 05, 2024

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant summary: GNE c.1132_1135delinsA (p.Leu378_His379delinsAsn) results in an in-frame deletion-insertion that is predicted to delete two and insert one amino acids from the protein and also cause changes in two amino acids. The variant was absent in 251446 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.1132_1135delinsA has been reported in the literature in individuals affected with Inclusion Body Myopathy 2 (Fisher_2006). These report(s) do not provide unequivocal conclusions about association of the variant with Inclusion Body Myopathy 2. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publication have been ascertained in the context of this evaluation (PMID: 19078806). ClinVar contains an entry for this variant (Variation ID: 558730). Based on the evidence outlined above, the variant was classified as uncertain significance.

GNE myopathy Uncertain:1

Jun 07, 2018

Counsyl

Significance: Uncertain significance

Review Status: no assertion criteria provided

Collection Method: clinical testing

This submission and the accompanying classification are no longer maintained by the submitter. For more information on current observations and classification, please contact variantquestions@myriad.com.

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		8.4
Mutation Taster		=0/200	disease causing

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1554660095; hg19: chr9-36229046;