Help

Hello, my name is Conrad! Conrad the bunny! Soon we will meet in other softwares as well developed by the programmers of Calcipath, to help you to get start the programs, and much more! Stay tuned fo the news!

Lets start with Calcipath!

1) What is this site and who is it for?

Calcipath helps provide a consistent, transparent interpretation of variants in the ABCC6 gene. It applies the Sherloc-style, refined, point-based logic of the 2015 ACMG–AMP guidelines with ABCC6-specific rules (e.g., NMD-aware LOF/splice handling, NBD/hotspot priorities, gnomAD homozygote flag, “low-penetrance” labels). It is intended for clinical geneticists, researchers, and data curators and NOT for patients, relatives or care givers.

2) Quick start

Open the Search page. Enter a variant into the “Variant ID / HGVS / Amino acid change” field (e.g., c.1171A>G or p.Arg391Gly). Results will appear below the form.
Or browse the Database list, which shows all curated ABCC6 variants (nucleotide/amino-acid change, enrichment, Fisher p-value).
Once you’ve found an interesting variant, click the small blue icon on the right of the Search page to pull in the data we store for that variant — or provide your own inputs if you prefer. The system also works with variants not present in the database; in that case, you’ll need to enter all data yourself.
Finally, click the blue Submit button at the bottom!

3) Search fields and what they mean

The following fields are available on the Search form; all can be freely combined.

Basic identifiers

• Variant ID / HGVS / Amino acid change – Search using HGVS at the nucleotide (c.) or protein (p.) level, or free text (e.g., Arg391Gly).
• Nucleotide change / Amino acid change / Gene Symbol – Separate fields for more targeted search (focus on ABCC6).

Population and cohort metrics

• Allele Frequency (AF) – gnomAD allele frequency.
• Homozygous Count – number of gnomAD homozygotes.
• Enrichment & Fisher – metrics comparing the patient cohort to gnomAD controls (the Database table shows the “Enrichment” label and the Fisher p-value). These also help recognize incomplete penetrance.

Clinical evidence

• Segregation Data (LOD) – tick this if at least “≥3 informative individuals from 1 family (weak)” is met; in recessive inheritance this often shifts 3LP → LP.
• Case Report Count – number of literature/clinical reports.
• Zygosity – proband genotype and the status of the other allele:
  • Homozygous
  • Heterozygous or Unknown
  • One variant is VUS not in cis
  • One variant is (Likely) Pathogenic not in cis
    These are particularly important for ABCC6 (recessive disease, in trans evidence).
• De Novo – Is the allele present in the parents?

In-silico (supportive, not decisive)

PolyPhen-2 (probably/possibly damaging, benign), MutationTaster (disease causing, polymorphism), MutationAssessor (High/Medium/Low/Neutral), Align-GVGD (C classes). In Sherloc, in-silico is supportive only; if you use functional evidence, in-silico does not add extra points.

Variant type (molecular context)

• Same amino acid substitution as (Likely) Pathogenic variant but different nucleotide change – PS1/PM5-like related-variant evidence.
• Affects residue critical for protein structure/function / Different missense at this residue is (Likely) Pathogenic / Located in functional domain or mutational hotspot / VUS reported at this residue – position/domain priors (in ABCC6, NBDs and exon 24 are highlighted).
• Nonsense / Frameshift / Missense / Large deletion / Synonymous – variant type; for LOF/splice, NMD-aware rules apply.
• Splice site – canonical sites (e.g., Intron 5' end GU, Intron/Exon 3' end AG, Exon first nucleotide mutation, Last G in exon mutation, A before last in exon mutation).

Functional data (experimental)

Strong/Weak Evidence – Impact observed / No impact observed – summary of functional assays. In Sherloc, a cap applies (by themselves they are not definitive), and clinical > functional has priority if there is conflict.

4) “Database” page — what does the table show?

List of all curated ABCC6 variants:
Nucleotide Change | Amino acid change | Enrichment | Fisher (p).
You can search within the table using your browser; for details, go to the Search page and enter the variant.

5) How does the system compute the result? (short)

Evidence contributes points separately in the pathogenic (P) and benign (B) directions; totals are compared to thresholds (e.g., LP ≥ 4P, P ≥ 5P; LB ≥ 3B, B ≥ 5B).

ABCC6-specific refinements:

• Handling of AF / “somewhat-high” range and gnomAD homozygote flag.
• NMD-aware LOF/splice rules.
• Domain/hotspot priors (NBD1/NBD2, exon 24), without double-counting.
• Low-penetrance labels (e.g., p.Arg391Gly, p.Val787Ile-type situations).
• Clinical > functional priority in case of conflict.

 

 

Results

What is this page for?

The Results page evaluates the selected variant(s) using Sherloc logic and shows all evidence in clear blocks (population, clinical/segregation, functional, in-silico), along with the final class (Pathogenic / Likely Pathogenic / VUS / 3LP / 3LB / Likely Benign / Benign).

What do I see at first glance? (header card)

• Final class: Pathogenic / Likely Pathogenic / VUS (with 3LP/3LB marker) / Likely Benign / Benign.
• Low-penetrance badge (if relevant): indicates a variant that is pathogenic but shows incomplete penetrance (e.g., R391G, V787I-type cases).
• P–B point bars: separate bars for the Pathogenic (P) and Benign (B) totals, with Sherloc thresholds:
  • LP ≥ 4P, P ≥ 5P
  • LB ≥ 3B, B ≥ 5B
• Short rationale: in 1–2 lines, which evidence drove the decision (e.g., “in trans + LOD 3.2”, “≥2 gnomAD hom.”, “exon 24 hotspot”, etc.).

How is the final class determined?

1. The system separately sums points in the P and B directions.
2. Thresholds are applied (LP ≥ 4P, P ≥ 5P; LB ≥ 3B, B ≥ 5B).
3. If there are substantial points on both sides, conflict resolution is applied: the program checks Enrichment and Fisher values and incomplete penetrance, and re-classifies based on the points obtained.
4. VUS split: within class 3, 3LP (closer to LP) and 3LB (closer to LB) are distinguished.

 

Where do I start if I want to run it again?

You typically arrive at the Results page from Search after entering/filtering the variant and launching the evaluation. (You can find the list of search fields in the “Search” help.)