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Gene → Transcript → Variant → Codon → Protein → Experiment

Protein Variant → Experiment Designer

Map protein variants and coding-DNA changes onto RefSeq/UniProt records, inspect sequence consequences, and move directly into PCR or 3D structure workflows.

Phase 6: source-linked dbSNP, ClinVar and gnomAD v4 annotations after exact genomic mapping. Phase 7: transcript-aware consequence and computational evidence synthesis using the validated HGVS context; no clinical classification is assigned. Phase 8: batch VCF analysis is available as a separate workflow. Phase 9: validated genomic alleles can be sent directly to variant-aware PCR/Sanger, allele-specific or indel-junction primer design.

Open Phase 8 Batch VCF Analysis

1. Choose target records

Gene symbol

Organism / species

RefSeq transcript Experiment-ready

Preferred when you need CDS, exon context, PCR/Sanger sequence or nucleotide-level analysis.

Use this when the transcript you need is not shown in the short dropdown list.

UniProt protein Protein fallback

Used for protein-level mapping and 3D follow-up when a suitable RefSeq CDS is unavailable.

Enter a gene and search RefSeq + UniProt records.

2. Enter variant

Variant

Supported: protein substitutions/deletions/duplications; coding substitutions; del, dup, ins, delins; and splice-site notation such as c.5152+1G>T. RefSeq is preferred for nucleotide-aware mapping; protein-only variants can fall back to UniProt.

3. Variant map

Choose a transcript to continue: multiple compatible RefSeq transcripts were found. Click Use in the transcript compatibility table; the Variant map will then be populated for that specific transcript.

Normalized variant—

Transcript—

Protein—

Exon—

CDS—

Protein effect—

Coding / codon consequence

—→

Reference protein context

—

Predicted mutant protein context

—

4. RefSeq transcript compatibility

Comprehensive transcript scan results will appear here.

Transcript-specific notation: the same c. or protein position can map differently across isoforms. When more than one transcript is compatible, choose the intended transcript explicitly rather than treating one compatible record as canonical.

Transcript	Status	Protein	RefSeq type	Mapping	Use

5. Genomic DNA validation

Select and map a transcript-specific c. variant to validate its genomic coordinate.

Chromosome—

Genomic RefSeq—

Genomic coordinate—

Reference validation—

Mapping source—

Genomic HGVS / SPDI

—

6. Database annotations

Exact genomic mapping is required before external database annotation.

dbSNPWaiting

—

RefSNP IDs are matched from the normalized genomic SPDI.

ClinVarWaiting

—

Aggregate classifications stay separated by germline, oncogenicity and somatic clinical-impact type.

gnomAD v4Waiting

—

Frequency is queried only after normalization to genomic VCF fields.

Research-use database evidence only. This section is not a diagnosis, prognosis, treatment recommendation, or proof of functional effect.

8. Experiment-ready sequence

Variant-centered transcript sequence

Experimental considerations