Day 1, evening
No genetics degree. No lab access. No budget. Just a laptop, a phone, and an AI agent (OpenClaw + Claude Opus 4.6) that can actually do things: download files, search databases, parse data, build sites. My job was asking questions. Good ones. Here's exactly what I asked and what came back.
1
I started with my son's genetic report
Michael's WES report from Hong Kong Children's Hospital (Lab No: 23C7500174, December 2022) listed two STRC variants. One was labeled "Pathogenic" (a whole gene deletion from his father, confirmed by MLPA). The other was labeled "Variant of Uncertain Significance" (a single letter change from his mother, confirmed by Sanger sequencing): NM_153700.2:c.4976A>C p.(Glu1659Ala). I needed to know: is this second variant actually harmful?
What you need: your child's genetic test report with the exact variant nomenclature (gene name, c. notation, p. notation).
2
I asked: where is this protein?
I asked Claude to look up the STRC protein. It searched UniProt and found the ID: Q7RTU9. Claude then pointed me to AlphaFold, which has the predicted 3D structure. The confidence score (pLDDT) at position 1659 was 95.69 out of 100, meaning the structure prediction at this spot is very reliable.
Step A: Go to
uniprot.org, search your gene name, note the UniProt accession ID
uniprot.org
Q7RTU9 · STRC_HUMAN
Stereocilin · 1,775 aa
Gene: STRC · Organism: Homo sapiens
alphafold.ebi.ac.uk
AF-Q7RTU9-F1 (v6)
pLDDT at pos 1659: 95.69
Very high confidence structure
3
I asked: is this mutation harmful? (the key discovery)
AlphaMissense is a tool by Google DeepMind that predicts whether a protein mutation is harmful. Claude downloaded the AlphaMissense predictions file for stereocilin and searched for "E1659A" (E = Glutamic acid, the original amino acid; A = Alanine, Michael's variant).
The result: 0.9016 out of 1.0 (Likely Pathogenic). Anything above 0.564 is considered likely harmful. I then checked all 19 other possible changes at position 1659. Every single one scored above 0.846. This means position 1659 is structurally critical: any change there breaks the protein.
Then: Open in Excel or Google Sheets, search for your variant (e.g. "E1659A"). Score > 0.564 = Likely Pathogenic
For other genes: Replace Q7RTU9 with your protein's UniProt ID in the URL
AF-Q7RTU9-F1-aa-substitutions.csv (filtered)
| protein_variant | am_pathogenicity | am_class |
| E1659A | 0.9016 | LPath |
| E1659D | 0.9483 | LPath |
| E1659G | 0.9191 | LPath |
| ... all 19 substitutions: LPath (0.846-0.999) |
4
I asked: is this position important across species?
If a position is important for the protein, it should be the same amino acid across different species. Claude pulled stereocilin sequences from 9 mammals on UniProt (human, mouse, rat, cow, monkey, pig, dog, bat, bear) and searched for the motif around position 1659 in each.
Result: 100% conserved. All 9 species have Glutamic acid (E) at this position. The surrounding 13-residue motif (PEIFTEIGTIAAG) is identical across ~80 million years of evolution. This is PP1 Supporting evidence under ACMG criteria.
Then: Download FASTA for each species, search for a unique motif near your variant position
Shortcut: If the amino acid + surrounding residues are identical across mammals, the position is conserved
5
We tried the standard tools (they failed)
Normally, geneticists use SIFT, PolyPhen-2, and CADD to check variants. Claude tried all three through the Ensembl VEP API. They all returned nothing for this variant.
The reason: STRC has a nearly identical "twin" gene next to it on chromosome 15 (a pseudogene called STRCP1) that confuses sequence-alignment-based tools. This is why AlphaMissense is uniquely important for STRC: it works from the protein's 3D structure, not from the DNA sequence, so the pseudogene doesn't affect it.
Note: If your gene doesn't have a pseudogene, SIFT/PolyPhen may work for you. Check your gene on NCBI first
6
I asked: does this add up to a reclassification?
ACMG/AMP guidelines (Richards et al., 2015) are the standard framework geneticists use to classify variants. Each piece of evidence gets a code and strength level. I learned the rules and applied them:
- PM3 (Moderate): The variant was found in trans with a known pathogenic deletion (one from each parent, confirmed by parental testing). ClinGen SVI rules
- PP3_Moderate (Moderate): Two concordant computational tools predict pathogenicity: AlphaMissense (0.9016) + REVEL (0.65). Upgraded from Supporting to Moderate per Pejaver et al. 2022
- PM2_Supporting (Supporting): Absent from gnomAD (0 alleles in 251,000+ individuals)
- PP1_Supporting (Supporting): Position 100% conserved across 9 mammalian species (see Step 4)
2 Moderate + 2 Supporting = Likely Pathogenic. Per ACMG combining rules (Table 5), this meets the threshold for Likely Pathogenic classification.
7
I wrote to the hospital
I compiled all evidence into a formal letter addressed to the Chemical Pathology Laboratory at Hong Kong Children's Hospital, requesting a reclassification review of the variant from VUS to Likely Pathogenic. I attached the AlphaMissense data, conservation analysis, and ACMG criteria breakdown. I also built this website so the evidence is transparent, reproducible, and accessible to anyone reviewing the case.
8
What happens next
If the hospital accepts the reclassification, Michael's molecular diagnosis will be confirmed: biallelic pathogenic STRC (DFNB16). This is a prerequisite for future gene therapy clinical trials. Dual-AAV gene therapy has already restored hearing in STRC-deficient mice (Iranfar et al., January 2026). Human trials are expected within 2-3 years. Michael will be 7-8 years old.
