rs1555706706

Variant names:

• chr19-12649967-TC-T
• rs1555706706
• NM_000528.4:c.2212delG

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1 PM2 PP5_Very_Strong

The NM_000528.4(MAN2B1):​c.2212delG​(p.Glu738ArgfsTer28) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★★). Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 30)
• Consequence: MAN2B1 NM_000528.4 frameshift
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:2
• Conservation: PhyloP100: -0.0110

Genes affected

MAN2B1 (HGNC:6826): (mannosidase alpha class 2B member 1) This gene encodes an enzyme that hydrolyzes terminal, non-reducing alpha-D-mannose residues in alpha-D-mannosides. Its activity is necessary for the catabolism of N-linked carbohydrates released during glycoprotein turnover and it is member of family 38 of glycosyl hydrolases. The full length protein is processed in two steps. First, a 49 aa leader sequence is cleaved off and the remainder of the protein is processed into 3 peptides of 70 kDa, 42 kDa (D) and 13/15 kDa (E). Next, the 70 kDa peptide is further processed into three peptides (A, B and C). The A, B and C peptides are disulfide-linked. Defects in this gene have been associated with lysosomal alpha-mannosidosis. Alternatively spliced transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Mar 2010]

ACMG classification

Verdict is Pathogenic. Variant got 18 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
• PP5: Variant 19-12649967-TC-T is Pathogenic according to our data. Variant chr19-12649967-TC-T is described in ClinVar as [Pathogenic]. Clinvar id is 520823.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAN2B1	NM_000528.4	c.2212delG	p.Glu738ArgfsTer28	frameshift_variant	Exon 18 of 24	ENST00000456935.7	NP_000519.2
MAN2B1	NM_001173498.2	c.2209delG	p.Glu737ArgfsTer28	frameshift_variant	Exon 18 of 24		NP_001166969.1
MAN2B1	XM_005259913.3	c.2215delG	p.Glu739ArgfsTer28	frameshift_variant	Exon 18 of 24		XP_005259970.1
MAN2B1	XM_047438841.1	c.1111delG	p.Glu371ArgfsTer28	frameshift_variant	Exon 11 of 17		XP_047294797.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAN2B1	ENST00000456935.7	c.2212delG	p.Glu738ArgfsTer28	frameshift_variant	Exon 18 of 24	1	NM_000528.4	ENSP00000395473.2
MAN2B1	ENST00000221363.8	c.2209delG	p.Glu737ArgfsTer28	frameshift_variant	Exon 18 of 24	1		ENSP00000221363.4
MAN2B1	ENST00000466794.5	n.2802delG		non_coding_transcript_exon_variant	Exon 16 of 22	2

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome Cov.: 34

GnomAD4 genome Cov.: 30

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Inborn genetic diseases Pathogenic:1

Nov 24, 2015

Ambry Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Deficiency of alpha-mannosidase Pathogenic:1

Sep 05, 2021

Genome-Nilou Lab

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.15		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1555706706; hg19: chr19-12760781;