Super-simple application of pathogenicity evidence during variant assessment in @deciphergenomics.bsky.social - even for complicated PVS1 in multiexon deletions where the frame is preserved - confirming a likely diagnosis.

Very cool new feature in @deciphergenomics.bsky.social - direct link from any missense variant to ProtVar @ebi.embl.org. This variant is in the binding site and likely interacts with the ligand, predicted using AlphaFold with AlphaFill!

The bespoke PubMed search on gene pages is now displayed in bold. This link opens a browser tab with a PubMed search displaying publications that include the gene of interest.

Descriptive names for gene and protein predictive scores are now displayed on gene pages to assist in demystifying these scores and making them easier to understand.

ClinGen Variant Curation Expert Panel Recommendations are now displayed more clearly on gene pages and in the pathogenicity evidence interface, especially for genes with recommendations for more than one disease @theacmg.bsky.social

Links to ProtVar are now available from the protein browser which provide functional and structural annotations for missense variants @ebi.embl.org

Mitochondrial gene predictive scores are now displayed on gene pages which indicate the observed depletion or enrichment of specific variants classes in @gnomad-project.bsky.social l‬ compared to a mitochondrial genome constraint model under neutrality selection.

DECIPHER version 11.34 has been released. See the new features at www.deciphergenomics.org #variantinterpretation

FASTKD5-related Leigh syndrome added to DDG2P. Biallelic FASTKD5 LoF variants cause an early- to late-onset Leigh syndrome associated with complex IV deficiency. www.ebi.ac.uk/gene2phenoty...

'UGGT1-related congenital disorder of glycosylation with neurodevelopmental impairment' added to DDG2P. Biallelic UGGT1 LoF variants cause a disorder characterised by developmental delay, intellectual disability, seizures, craniofacial dysmorphism, and microcephaly. See www.ebi.ac.uk/gene2phenoty...

18 additional @gnomad-project.bsky.social short tandem repeats are now displayed; 9 recently discovered and 9 which are not currently linked to rare diseases but have historically appeared in various catalogs as suspected disease-causing loci.

‪Additional functional data from Multiplexed Assays of Variant Effect (MAVEs) are now displayed on functional tabs. Previously only published datasets were displayed, now datasets with a preprint are available @varianteffect.bsky.social

DECIPHER version 11.33 has been released. See the new features at www.deciphergenomics.org #variantinterpretation

Unravel the complexities of genome variation with our FREE online course! #FLGenomicVariantsDiversity 🗓️ Starts: 7 July Learn how to get the most from #genomics data from diverse populations, using variant classification and interpretation approaches. #GenomeVariation🧬 📎bit.ly/3R7G7aK

DECIPHER and #clinvar variants with a predicted molecular consequence of splice_donor_region_variant and splice_polypyrimidine_tract_variant are now displayed on the protein browser. These are displayed as pink triangles.

‪@gnomad-project.bsky.social‬ v4.1 sequence variant data is now displayed; re-annotated using @ensembl.bsky.social‬ Variant Effect Predictor so molecular consequences reflect the gene build on the DECIPHER website. Data will be re-annotated in the future to ensure the annotations remain current‬

DECIPHER version 11.32 has been released. See the new features at www.deciphergenomics.org #variantinterpretation

Thanks for capturing this and thanks to the workshop organiserat #ESHG2025☺️ DECIPHER is an amazing example of how keeping genomic data patient centred makes it better! That is all 🎤 @deciphergenomics.bsky.social (COI see my bio)

Ear disorders curated by Gene2Phenotype (G2P) are now displayed across the website. This includes curations for 87 genes and 97 Locus-Genotype-Mechanism-Disease-Evidence (LGMDE) threads @gene2phenotype.bsky.social

Cancer case frequency data compiled by the National Disease Registration Service from diagnostic laboratories in England is now displayed on the protein browser. Data is available for ~4,500 variants in 13 cancer susceptibility genes including BRCA1, BRCA2, MSH2, PTEN and SMAD4.

Human Developmental Cell Atlas (HDCA) expression data is now displayed. Expression is displayed in 12 sections of a 6-7 post-conception week human embryo, alongside a sagittal view which displays the region of the embryo represented by each section @mhaniffa.bsky.social

DECIPHER version 11.31 has been released. See the new features at www.deciphergenomics.org #variantinterpretation

Submit your abstract for the Curating the Clinical Genome conference - deadline is tomorrow.

Can you spare 5 minutes to help shape the future development of DECIPHER? Your views are extremely important to us. Please access our user survey here: docs.google.com/forms/d/e/1F...

Can you spare 5 minutes to help shape the future development of DECIPHER? Your views are extremely important to us. Please access our user survey here: docs.google.com/forms/d/e/1F...

The pathogenicity of DECIPHER and ClinVar variants are now displayed in bold on variant and protein variant pages to make it clearer if the variant has been classified as being pathogenic or benign

The display of @gene2phenotype.bsky.social (G2P) data has been updated to reflect the new data structure of curated Locus-Genotype-Mechanism-Disease-Evidence threads which allow for precise definition of the clinical phenotype and molecular basis of a given condition @ebi.embl.org

DECIPHER version 11.30 has been released. See the new features at www.deciphergenomics.org #variantinterpretation

DECIPHER is proud to have made an impact on rare disease research over the last 20 years; more than 4000 publications have cited the platform.

Congratulations to our G2P colleagues on the new website and updated disease-models, which now include more detailed disease mechanism information.

🎉 Registration is now open for the Mutational Scanning Symposium "Mapping and Modelling Variant Effects at Scale" #VariantEffect25 @ibecbarcelona.eu ℹ️ events.ibecbarcelona.eu/mutational-s...

Registration is now open for our Curating the Clinical Genome Conference! #CCG2025 🗓️Dates: 11 - 13 June 2025 If you are interested in shaping best practices for the clinical use of #GenomicsData, then this is the conference for you! 🧬 🗣️ Keynote: @heidirehm.bsky.social 📎Info: bit.ly/4gt4EB6

DECIPHER users can now search for patient matches in Boston Children’s Hospital seqr in addition to PhenomeCentral, Broad seqr, GeneMatcher, RD-connect and MyGene2 using Matchmaker Exchange

A @gnomad-project.bsky.social Short Tandem Repeat track is now available on the genome browser which displays information about 60 disease associated repeat loci. The associated diseases are displayed along with the normal and pathogenic repeat lengths, and links to STRipy

Protein predictive scores which predict the likelihood that the protein is associated with a dominant-negative, gain-of-function or loss-of-function mechanism are displayed. Curated literature support for a molecular disease mechanism is also shown jmarshlab.bsky.social @mbadonyi.bsky.social

The prevalence for cardiomyopathies is also now displayed for genes associated with cardiac disorders @jamesware.bsky.social @kathrynmcgurk.bsky.social

Cardiac case/control cohort data, which demonstrates the confidence of cardiac gene-phenotype relationships associated with specific variant classes, has been updated; more variant classes e.g. canonical splice site variants @jamesware.bsky.social @kathrynmcgurk.bsky.social

Estimated population penetrance for variants associated with cardiomyopathies are now displayed alongside cardiac allele frequencies. This information is useful when considering secondary findings @jamesware.bsky.social @kathrynmcgurk.bsky.social

Cancer case frequency data compiled by the National Disease Registration Service from diagnostic laboratories in England is now displayed. Nearly 4,500 variants in 13 cancer susceptibility genes including BRCA1, BRCA2, MSH2, PTEN and SMAD4.

DECIPHER version 11.29 has been released. See the new features at www.deciphergenomics.org #variantinterpretation

Happy 20th Birthday DECIPHER The DECIPHER team celebrating the platform facilitating variant classification, patient diagnosis and empowering rare disease research for 20 years. @malloryfreeberg.bsky.social @mehurles.bsky.social @helenvfirth.bsky.social