3-187253197-C-A

Position:

• chr3-187253197-C-A

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_139125.4(MASP1):​c.863G>T​(p.Arg288Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. 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. R288Q) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: MASP1 NM_139125.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.89

Genes affected

MASP1 (HGNC:6901): (MBL associated serine protease 1) This gene encodes a serine protease that functions as a component of the lectin pathway of complement activation. The complement pathway plays an essential role in the innate and adaptive immune response. The encoded protein is synthesized as a zymogen and is activated when it complexes with the pathogen recognition molecules of lectin pathway, the mannose-binding lectin and the ficolins. This protein is not directly involved in complement activation but may play a role as an amplifier of complement activation by cleaving complement C2 or by activating another complement serine protease, MASP-2. The encoded protein is also able to cleave fibrinogen and factor XIII and may may be involved in coagulation. A splice variant of this gene which lacks the serine protease domain functions as an inhibitor of the complement pathway. Alternate splicing results in multiple transcript variants.[provided by RefSeq, Apr 2010]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.21844804).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MASP1	NM_139125.4	c.863G>T	p.Arg288Leu	missense_variant	6/11	ENST00000296280.11
MASP1	NM_001879.6	c.863G>T	p.Arg288Leu	missense_variant	6/16	ENST00000337774.10
MASP1	NM_001031849.3	c.863G>T	p.Arg288Leu	missense_variant	6/9
MASP1	NR_033519.2	n.736G>T		non_coding_transcript_exon_variant	5/10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MASP1	ENST00000296280.11	c.863G>T	p.Arg288Leu	missense_variant	6/11	1	NM_139125.4
MASP1	ENST00000337774.10	c.863G>T	p.Arg288Leu	missense_variant	6/16	1	NM_001879.6	P1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ExAC AF: 0.00000824 AC: 1

EpiCase AF: 0.0000545

EpiControl AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.16
BayesDel_addAF	Benign	-0.25	T
BayesDel_noAF	Benign	-0.59
CADD	Benign	18
DANN	Uncertain	0.98
DEOGEN2	Benign	0.11	T;.;.;.;T
Eigen	Benign	-0.45
Eigen_PC	Benign	-0.31
FATHMM_MKL	Benign	0.57	D
LIST_S2	Uncertain	0.90	D;D;D;D;D
M_CAP	Benign	0.0046	T
MetaRNN	Benign	0.22	T;T;T;T;T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	0.72	N;N;.;N;.
MutationTaster	Benign	0.79	D;D;D;D;D
PrimateAI	Benign	0.38	T
PROVEAN	Benign	-1.7	N;N;D;N;N
REVEL	Benign	0.066
Sift	Benign	0.25	T;T;T;T;T
Sift4G	Benign	0.33	T;T;T;T;T
Polyphen		0.029	B;B;B;B;B
Vest4		0.18
MutPred		0.67		Gain of glycosylation at S293 (P = 0.0074);Gain of glycosylation at S293 (P = 0.0074);.;Gain of glycosylation at S293 (P = 0.0074);.;
MVP		0.27
MPC		0.15
ClinPred		0.31	T
GERP RS		2.0
Varity_R		0.22
gMVP		0.53

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

Other links and lift over

dbSNP: rs116001173; hg19: chr3-186970985;