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Calculate Local Constraint

Variant Local Constraint

Calculate local constraint scores of the region around a variant. This can be used to test if a variant is at a position in a region of a gene that is subject to constrained selection, even if the entire gene is not constrained.

NOTE: This tool has not been validated for clinical use. Use only for research use, or in consultation with a clinical bioinformatician or clinical geneticist in the context of other clinical evidence.

Gene:

Position: or Range: -

You do not need to provide an exact nucleotide change, only the position

Optional:

ENST:

ENSG:

UniProt:

The script has defaults (below) of these stored or attempts to look them up if they are not specified.

Citation

If you wish to use this tool, please cite the following publication:
Cross, E., Duncan-Flavell, P. J., Howarth, R. J., Crooks, R. O., Thomas, N. S. and Bunyan, D. J. (2020) Screening of a large PAX6 cohort identified many novel variants and emphasises the importance of the paired and homeobox domains. Eur J Med Genet. 63: 103940. PubMed: 32360764 - DOI: 10.1016/j.ejmg.2020.103940

For the source code, including latest code revisions, and issue reporting, please refer to the Git repository

Default Gene IDs

Default gene IDs used in the local constraint tool

Gene Symbol ENST ENSG UniProt
ADAMTS10ENST00000270328ENSG00000142303Q9H324
ADAMTS17ENST00000268070ENSG00000140470Q8TE56
ADAMTSL2ENST00000354484ENSG00000197859Q86TH1
ADAMTSL4ENST00000271643ENSG00000143382Q6UY14
ARENST00000374690ENSG00000169083P10275
ARXENST00000379044ENSG00000004848Q96QS3
ATRXENST00000373344ENSG00000085224P46100
BRAFENST00000288602ENSG00000157764P15056
BRCA1ENST00000471181ENSG00000012048P46736
BRCA2ENST00000544455ENSG00000139618P51587
CBLENST00000264033ENSG00000110395P22681
CBSENST00000398165ENSG00000160200P35520
CBX2ENST00000310942ENSG00000173894Q14781
COL1A1ENST00000225964ENSG00000108821P02452
COL1A2ENST00000297268ENSG00000164692P08123
COL3A1ENST00000304636ENSG00000168542P02461
COL5A1ENST00000371817ENSG00000130635P20908
COL5A2ENST00000374866ENSG00000204262P05997
CYP11A1ENST00000268053ENSG00000140459P05108
CYP11B1ENST00000292427ENSG00000160882P15538
CYP17A1ENST00000369887ENSG00000148795P05093
CYP19A1ENST00000396402ENSG00000137869P11511
CYP21A2ENST00000418967ENSG00000231852P08686
DHCR7ENST00000355527ENSG00000172893Q9UBM7
DHHENST00000266991ENSG00000139549O43323
DMRT1ENST00000382276ENSG00000137090Q9Y5R6
FBN1ENST00000316623ENSG00000166147P35555
FBN2ENST00000508053ENSG00000138829P35556
HRASENST00000451590ENSG00000174775P01112
HSD17B2ENST00000199936ENSG00000086696P37059
HSD17B3ENST00000375263ENSG00000130948P37058
HSD3B2ENST00000543831ENSG00000203859P26439
KRASENST00000256078ENSG00000133703P01116
LHCGRENST00000294954ENSG00000138039P22888
MAMLD1ENST00000432680ENSG00000013619Q13495
MAP2K1ENST00000307102ENSG00000169032Q02750
MAP2K2ENST00000262948ENSG00000126934P36507
MAP3K1ENST00000399503ENSG00000095015Q13233
MLH1ENST00000231790ENSG00000076242P40692
MSH2ENST00000233146ENSG00000095002P43246
MYH11ENST00000396324ENSG00000133392P35749
NF1ENST00000358273ENSG00000196712P21359
NR0B1ENST00000378970ENSG00000169297P51843
NR5A1ENST00000373588ENSG00000136931Q13285
NRASENST00000369535ENSG00000213281P01111
PORENST00000461988ENSG00000127948P16435
PTENENST00000371953ENSG00000171862P60484
PTPN11ENST00000351677ENSG00000179295Q06124
RAD51CENST00000337432ENSG00000108384O43502
RAD51DENST00000590016ENSG00000185379O75771
RAF1ENST00000251849ENSG00000132155P04049
RASA1ENST00000274376ENSG00000145715P20936
RSPO1ENST00000356545ENSG00000169218Q2MKA7
SHOC2ENST00000369452ENSG00000108061Q9UQ13
SLC2A10ENST00000359271ENSG00000197496O95528
SMAD3ENST00000327367ENSG00000166949P84022
SOS1ENST00000426016ENSG00000115904Q07889
SOX9ENST00000245479ENSG00000125398P48436
SPRED1ENST00000299084ENSG00000166068Q7Z699
SRYENST00000383070ENSG00000184895Q05066
STARENST00000276449ENSG00000147465P49675
TGFB2ENST00000366929ENSG00000092969P61812
TGFBR1ENST00000374994ENSG00000106799P36897
TGFBR2ENST00000359013ENSG00000163513P37173
WNT4ENST00000290167ENSG00000162552P56705

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