11-102606578-C-T
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBS1_SupportingBS2
The NM_004771.4(MMP20):c.910G>A(p.Ala304Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00234 in 1,613,968 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_004771.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00169 AC: 257AN: 152120Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00156 AC: 393AN: 251322Hom.: 0 AF XY: 0.00152 AC XY: 207AN XY: 135848
GnomAD4 exome AF: 0.00240 AC: 3515AN: 1461730Hom.: 3 Cov.: 31 AF XY: 0.00241 AC XY: 1754AN XY: 727162
GnomAD4 genome AF: 0.00169 AC: 257AN: 152238Hom.: 0 Cov.: 32 AF XY: 0.00144 AC XY: 107AN XY: 74446
ClinVar
Submissions by phenotype
not provided Uncertain:1
This sequence change replaces alanine with threonine at codon 304 of the MMP20 protein (p.Ala304Thr). The alanine residue is highly conserved and there is a small physicochemical difference between alanine and threonine. This variant is present in population databases (rs148818720, ExAC 0.2%). This variant has been observed in individual(s) with melogenesis imperfecta (PMID: 19966041). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 301942). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). Experimental studies have shown that this variant affects MMP20 function (PMID: 19966041). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Amelogenesis imperfecta hypomaturation type 2A2 Uncertain:1
The MMP20 c.910G>A (p.Ala304Thr) missense variant has been reported in a single case study in which it was found in a homozygous state in two siblings whose parents were both heterozygous carriers of the variant (Lee et al. 2010). In vitro functional experiments showed that this variant produces a protein that is catalytically active, but has decreased expression compared to wild type MMP20. The p.Ala304Thr variant was absent from 100 controls and is reported at a frequency of 0.00298 in the European population of the 1000 Genomes Project. The evidence for this variant is limited. The p.Ala304Thr variant is therefore classified as a variant of unknown significance but suspicious for pathogenicity for amelogenesis imperfecta. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at