Genetic Variant MBL2:p.Arg52Ser (chr10-52771481-CG-GA) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is . The variant received 0 ACMG points: 0P and 0B.

The NM_001378373.1(MBL2):c.154_155delCGinsTC(p.Arg52Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R52C) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)

Consequence

MBL2
NM_001378373.1 missense

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.972

Publications

0 publications found

Variant links:

Genes affected

MBL2 (HGNC:6922): (mannose binding lectin 2) This gene encodes the soluble mannose-binding lectin or mannose-binding protein found in serum. The protein encoded belongs to the collectin family and is an important element in the innate immune system. The protein recognizes and binds to mannose and N-acetylglucosamine on many microorganisms, including bacteria, yeast, and viruses including influenza virus, HIV and SARS-CoV. This binding activates the classical complement pathway. Deficiencies of this gene have been associated with susceptibility to autoimmune and infectious diseases. [provided by RefSeq, Jun 2020]

MBL2 Gene-Disease associations (from GenCC):

mannose-binding lectin deficiency
Inheritance: AD Classification: LIMITED Submitted by: PanelApp Australia

MBL2 links:

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new If you want to explore the variant's impact on the transcript NM_001378373.1, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001378373.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
MBL2	NM_001378373.1	MANE Select	c.154_155delCGinsTC	p.Arg52Ser	missense	N/A	NP_001365302.1	P11226
MBL2	NM_000242.3		c.154_155delCGinsTC	p.Arg52Ser	missense	N/A	NP_000233.1	P11226
MBL2	NM_001378374.1		c.154_155delCGinsTC	p.Arg52Ser	missense	N/A	NP_001365303.1	P11226

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
MBL2	ENST00000674931.1	MANE Select	c.154_155delCGinsTC	p.Arg52Ser	missense	N/A	ENSP00000502789.1	P11226
MBL2	ENST00000373968.3	TSL:1	c.154_155delCGinsTC	p.Arg52Ser	missense	N/A	ENSP00000363079.3	P11226
MBL2	ENST00000675947.1		c.154_155delCGinsTC	p.Arg52Ser	missense	N/A	ENSP00000502615.1	P11226

Frequencies

GnomAD3 genomes

Cov.:

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

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.97

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over