16-3050128-C-T
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_022468.5(MMP25):c.352C>T(p.Arg118*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000448 in 1,606,278 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: 𝑓 0.00033 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00046 ( 2 hom. )
Consequence
MMP25
NM_022468.5 stop_gained
NM_022468.5 stop_gained
Scores
2
3
2
Clinical Significance
Conservation
PhyloP100: 0.399
Genes affected
MMP25 (HGNC:14246): (matrix metallopeptidase 25) 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 MMPs are secreted as inactive proproteins which are activated when cleaved by extracellular proteinases. However, the protein encoded by this gene is a member of the membrane-type MMP (MT-MMP) subfamily, attached to the plasma membrane via a glycosylphosphatidyl inositol anchor. In response to bacterial infection or inflammation, the encoded protein is thought to inactivate alpha-1 proteinase inhibitor, a major tissue protectant against proteolytic enzymes released by activated neutrophils, facilitating the transendothelial migration of neutrophils to inflammatory sites. The encoded protein may also play a role in tumor invasion and metastasis through activation of MMP2. The gene has previously been referred to as MMP20 but has been renamed MMP25. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BS2
High Homozygotes in GnomAdExome4 at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MMP25 | NM_022468.5 | c.352C>T | p.Arg118* | stop_gained | 3/10 | ENST00000336577.9 | NP_071913.1 | |
MMP25 | XM_024450391.2 | c.250C>T | p.Arg84* | stop_gained | 2/9 | XP_024306159.1 | ||
MMP25 | XM_017023561.2 | c.352C>T | p.Arg118* | stop_gained | 3/6 | XP_016879050.1 | ||
MMP25 | XM_024450390.2 | c.232+2581C>T | intron_variant | XP_024306158.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MMP25 | ENST00000336577.9 | c.352C>T | p.Arg118* | stop_gained | 3/10 | 1 | NM_022468.5 | ENSP00000337816.4 |
Frequencies
GnomAD3 genomes AF: 0.000329 AC: 50AN: 152186Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000362 AC: 90AN: 248962Hom.: 0 AF XY: 0.000431 AC XY: 58AN XY: 134708
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GnomAD4 exome AF: 0.000460 AC: 669AN: 1453974Hom.: 2 Cov.: 33 AF XY: 0.000453 AC XY: 327AN XY: 721836
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GnomAD4 genome AF: 0.000328 AC: 50AN: 152304Hom.: 0 Cov.: 32 AF XY: 0.000363 AC XY: 27AN XY: 74472
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Mendelian syndromes with cleft lip/palate Uncertain:1
Uncertain significance, no assertion criteria provided | research | Faculty of Pharmacy, University of Ljubljana | - | - - |
Computational scores
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Name
Calibrated prediction
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BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
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DANN
Uncertain
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Uncertain
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Uncertain
FATHMM_MKL
Benign
N
Vest4
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Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at