rs1417381110
Variant summary
Our verdict is Likely pathogenic. The variant received 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_004530.6(MMP2):c.41T>C(p.Leu14Pro) variant causes a missense change. The variant allele was found at a frequency of 0.00000685 in 1,605,012 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004530.6 missense
Scores
Clinical Significance
Conservation
Publications
- multicentric osteolysis, nodulosis, and arthropathyInheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics
- multicentric osteolysis-nodulosis-arthropathy spectrumInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Our verdict: Likely_pathogenic. The variant received 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MMP2 | NM_004530.6 | c.41T>C | p.Leu14Pro | missense_variant | Exon 1 of 13 | ENST00000219070.9 | NP_004521.1 | |
MMP2 | NM_001302508.1 | c.-76+555T>C | intron_variant | Intron 1 of 12 | NP_001289437.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MMP2 | ENST00000219070.9 | c.41T>C | p.Leu14Pro | missense_variant | Exon 1 of 13 | 1 | NM_004530.6 | ENSP00000219070.4 | ||
MMP2 | ENST00000570308.5 | c.-75-3389T>C | intron_variant | Intron 2 of 13 | 1 | ENSP00000461421.1 | ||||
MMP2 | ENST00000568715.5 | c.-76+555T>C | intron_variant | Intron 1 of 3 | 4 | ENSP00000457949.1 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152090Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.00 AC: 0AN: 226698 AF XY: 0.00
GnomAD4 exome AF: 0.00000688 AC: 10AN: 1452922Hom.: 0 Cov.: 31 AF XY: 0.00000692 AC XY: 5AN XY: 722198 show subpopulations
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152090Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74302 show subpopulations
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.41T>C (p.L14P) alteration is located in exon 1 (coding exon 1) of the MMP2 gene. This alteration results from a T to C substitution at nucleotide position 41, causing the leucine (L) at amino acid position 14 to be replaced by a proline (P). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at