10-52771601-A-G

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3

The NM_001378373.1(MBL2):​c.35T>C​(p.Leu12Pro) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)

Consequence

MBL2
NM_001378373.1 missense

Scores

1
11
7

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.21
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]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 3 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.825

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
MBL2NM_001378373.1 linkc.35T>C p.Leu12Pro missense_variant 2/5 ENST00000674931.1 NP_001365302.1
MBL2NM_000242.3 linkc.35T>C p.Leu12Pro missense_variant 1/4 NP_000233.1 P11226
MBL2NM_001378374.1 linkc.35T>C p.Leu12Pro missense_variant 2/5 NP_001365303.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
MBL2ENST00000674931.1 linkc.35T>C p.Leu12Pro missense_variant 2/5 NM_001378373.1 ENSP00000502789.1 P11226
MBL2ENST00000373968.3 linkc.35T>C p.Leu12Pro missense_variant 1/41 ENSP00000363079.3 P11226
MBL2ENST00000675947.1 linkc.35T>C p.Leu12Pro missense_variant 2/5 ENSP00000502615.1 P11226

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
32
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.27
BayesDel_addAF
Uncertain
0.11
D
BayesDel_noAF
Uncertain
-0.070
CADD
Uncertain
24
DANN
Uncertain
0.98
DEOGEN2
Benign
0.32
T
Eigen
Uncertain
0.35
Eigen_PC
Uncertain
0.31
FATHMM_MKL
Uncertain
0.79
D
LIST_S2
Benign
0.41
T
M_CAP
Benign
0.017
T
MetaRNN
Pathogenic
0.83
D
MetaSVM
Benign
-0.31
T
MutationAssessor
Uncertain
2.5
M
PrimateAI
Benign
0.46
T
PROVEAN
Uncertain
-3.6
D
REVEL
Uncertain
0.59
Sift
Uncertain
0.0090
D
Sift4G
Uncertain
0.021
D
Polyphen
1.0
D
Vest4
0.66
MutPred
0.69
Gain of loop (P = 0.0045);
MVP
0.81
MPC
0.42
ClinPred
0.92
D
GERP RS
3.7
Varity_R
0.78
gMVP
0.63

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs72661127; hg19: chr10-54531361; API