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GeneBe

rs17576

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_004994.3(MMP9):c.836A>C(p.Gln279Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD Genomes project. In-silico tool predicts a benign outcome for this variant. 12/19 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. Q279R) has been classified as Benign.

Frequency

Genomes: not found (cov: 31)

Consequence

MMP9
NM_004994.3 missense

Scores

2
17

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.23
Variant links:
Genes affected
MMP9 (HGNC:7176): (matrix metallopeptidase 9) Proteins of the matrix metalloproteinase (MMP) family are involved in the breakdown of extracellular matrix in normal physiological processes, such as embryonic development, reproduction, and tissue remodeling, as well as in disease processes, such as arthritis and metastasis. Most MMP's are secreted as inactive proproteins which are activated when cleaved by extracellular proteinases. The enzyme encoded by this gene degrades type IV and V collagens. Studies in rhesus monkeys suggest that the enzyme is involved in IL-8-induced mobilization of hematopoietic progenitor cells from bone marrow, and murine studies suggest a role in tumor-associated tissue remodeling. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.23929572).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MMP9NM_004994.3 linkuse as main transcriptc.836A>C p.Gln279Pro missense_variant 6/13 ENST00000372330.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MMP9ENST00000372330.3 linkuse as main transcriptc.836A>C p.Gln279Pro missense_variant 6/131 NM_004994.3 P1

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD4 exome
Cov.:
61
GnomAD4 genome
Cov.:
31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.37
BayesDel_addAF
Benign
-0.15
T
BayesDel_noAF
Benign
-0.46
Cadd
Benign
19
Dann
Uncertain
0.99
DEOGEN2
Benign
0.13
T
Eigen
Benign
0.032
Eigen_PC
Benign
-0.0083
FATHMM_MKL
Benign
0.62
D
LIST_S2
Benign
0.82
T
M_CAP
Benign
0.0078
T
MetaRNN
Benign
0.24
T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
0.90
L
MutationTaster
Benign
0.83
N
PrimateAI
Benign
0.26
T
PROVEAN
Benign
-1.4
N
REVEL
Benign
0.12
Sift
Benign
0.20
T
Sift4G
Benign
0.16
T
Polyphen
0.94
P
Vest4
0.20
MutPred
0.56
Loss of stability (P = 0.0339);
MVP
0.63
ClinPred
0.56
D
GERP RS
2.7
Varity_R
0.20
gMVP
0.93

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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: rs17576; hg19: chr20-44640225; API