Resource
| Id | hg19/scores/MPC |
|---|---|
| Type | allele_score |
| Version | 0 |
| Summary | MPC (Missense badness, PolyPhen-2, and Constraint) is a composite score that predicts the impact of missense variants. |
| Description |
A deleteriousness prediction score for missense variants based on regional missense constraint. The range of MPC score is 0 to 5. The larger the score, the more likely the variant is pathogenic. Given increasing numbers of patients who are undergoing exome or genome sequencing, it is critical to establish tools and methods to interpret the impact of genetic variation. While the ability to predict deleteriousness for any given variant is limited, missense variants remain a particularly challenging class of variation to interpret, since they can have drastically different effects depending on both the precise location and specific amino acid substitution of the variant. In order to better evaluate missense variation, we leveraged the exome sequencing data of 60,706 individuals from the Exome Aggregation Consortium (ExAC) dataset to identify sub-genic regions that are depleted of missense variation. We further used this depletion as part of a novel missense deleteriousness metric named MPC. We applied MPC to de novo missense variants and identified a category of de novo missense variants with the same impact on neurodevelopmental disorders as truncating mutations in intolerant genes, supporting the value of incorporating regional missense constraint in variant interpretation. Details see doi: http://dx.doi.org/10.1101/148353. TODO tabix -s 1 -b 2 -e 2 -f fordistconstraintofficialmpcvalues_v2.txt.gz |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| MPC | float |
mpc |
Missense badness, PolyPhen-2, and Constraint.
A deleteriousness prediction score for missense variants"
Small values desc: less pathogenic
Large values desc: more pathogenic
|
 |
[0.000246, 5] |
|
n counts alleles; sd is the population standard deviation.
Alleles
| Chromosome | Alleles | substitution % | insertion % | deletion % | complex % | other % |
|---|---|---|---|---|---|---|
| all chromosomes | 66939306 | 100.00% | 0.00% | 0.00% | 0.00% | 0.00% |
| chr1 | 6885743 | 100.00% | 0.00% | 0.00% | 0.00% | 0.00% |
| chr2 | 4994791 | 100.00% | 0.00% | 0.00% | 0.00% | 0.00% |
| chr3 | 3993500 | 100.00% | 0.00% | 0.00% | 0.00% | 0.00% |
| chr4 | 2706911 | 100.00% | 0.00% | 0.00% | 0.00% | 0.00% |
| chr5 | 3157386 | 100.00% | 0.00% | 0.00% | 0.00% | 0.00% |
| chr6 | 3414396 | 100.00% | 0.00% | 0.00% | 0.00% | 0.00% |
| chr7 | 3001885 | 100.00% | 0.00% | 0.00% | 0.00% | 0.00% |
| chr8 | 2177691 | 100.00% | 0.00% | 0.00% | 0.00% | 0.00% |
| chr9 | 2634730 | 100.00% | 0.00% | 0.00% | 0.00% | 0.00% |
| chr10 | 2615322 | 100.00% | 0.00% | 0.00% | 0.00% | 0.00% |
| chr11 | 4006782 | 100.00% | 0.00% | 0.00% | 0.00% | 0.00% |
| chr12 | 3637477 | 100.00% | 0.00% | 0.00% | 0.00% | 0.00% |
| chr13 | 1213739 | 100.00% | 0.00% | 0.00% | 0.00% | 0.00% |
| chr14 | 2129683 | 100.00% | 0.00% | 0.00% | 0.00% | 0.00% |
| chr15 | 2402221 | 100.00% | 0.00% | 0.00% | 0.00% | 0.00% |
| chr16 | 2598535 | 100.00% | 0.00% | 0.00% | 0.00% | 0.00% |
| chr17 | 3842558 | 100.00% | 0.00% | 0.00% | 0.00% | 0.00% |
| chr18 | 1079934 | 100.00% | 0.00% | 0.00% | 0.00% | 0.00% |
| chr19 | 4283620 | 100.00% | 0.00% | 0.00% | 0.00% | 0.00% |
| chr20 | 1597262 | 100.00% | 0.00% | 0.00% | 0.00% | 0.00% |
| chr21 | 670717 | 100.00% | 0.00% | 0.00% | 0.00% | 0.00% |
| chr22 | 1284950 | 100.00% | 0.00% | 0.00% | 0.00% | 0.00% |
| chrX | 2561816 | 100.00% | 0.00% | 0.00% | 0.00% | 0.00% |
| chrY | 47657 | 100.00% | 0.00% | 0.00% | 0.00% | 0.00% |
Substitution matrix
| ref → alt | A | C | G | T |
|---|---|---|---|---|
| A | 0 0.00% | 6025014 9.00% | 5102231 7.62% | 5582556 8.34% |
| C | 5740988 8.58% | 0 0.00% | 6471320 9.67% | 4561529 6.81% |
| G | 4546616 6.79% | 6451178 9.64% | 0 0.00% | 5725854 8.55% |
| T | 5590888 8.35% | 5106493 7.63% | 6034639 9.02% | 0 0.00% |
Indel lengths
| alleles | min | max | mean | median | |
|---|---|---|---|---|---|
| insertions | 0 | ||||
| deletions | 0 |
no insertions
no deletions
Complex alleles
no complex alleles
Files
| Filename | Size | md5 |
|---|---|---|
| fordist_constraint_official_mpc_values_v2.txt.gz | 2.26 GB | a208ddc5f6b1d95afd9f76ac6b22f9c4 |
| fordist_constraint_official_mpc_values_v2.txt.gz.sha | 230.0 B | ad7119f38b88bc99fd24cdd1dd045bd1 |
| fordist_constraint_official_mpc_values_v2.txt.gz.tbi | 723.86 KB | 877cb8feebc49c22b6956928fb77f5b8 |
| genomic_resource.yaml | 2.48 KB | 176d2f8b654d4f4ea8bc751a1af9d27b |
| statistics/ |