Private Research DFNB16

STRC p.(Glu1659Ala)
Variant Pathogenicity Analysis

Computational evidence supporting reclassification of NM_153700.2(STRC):c.4976A>C from Variant of Uncertain Significance (VUS) to Likely Pathogenic. Includes AlphaMissense prediction, AlphaFold structural context, ACMG criteria, and gene therapy landscape.

AlphaMissense

0.9016

Likely Pathogenic

AlphaFold pLDDT

95.69

Very high confidence

REVEL Score

0.65

Predicted deleterious

gnomAD Frequency

0

Absent from controls

AlphaMissense Saturation

Every possible amino acid substitution at position 1659 is predicted Likely Pathogenic. This position is structurally invariant: any change breaks the protein.

EW

0.9997

EF

0.9992

EP

0.9985

EC

0.9984

EY

0.9981

EL

0.9929

EH

0.9927

EI

0.9923

EM

0.9909

EN

0.9822

ET

0.9666

EV

0.9664

ER

0.9634

ED

0.9483

ES

0.9433

EK

0.9272

EG

0.9191

EA

0.9016 MISHA

EQ

0.8460

Threshold: Likely Pathogenic > 0.564 | Ambiguous 0.340-0.564 | Likely Benign < 0.340

3D Protein Structure

Stereocilin (Q7RTU9, 1775 aa) from AlphaFold v6. Position E1659 highlighted in magenta. Drag to rotate, scroll to zoom.

Full Protein

Color: pLDDT confidence (blue=high, red=low)

E1659 Close-up

Glutamic acid side chain shown as sticks

Wildtype: Glutamic Acid (E)

Charge: Negative (-1)
Side chain volume: 138.4 A3
Hydrogen bond capacity: Donor + Acceptor
Role: Salt bridges, electrostatic interactions

Mutant: Alanine (A)

Charge: Neutral (0)
Side chain volume: 67.0 A3 (-52%)
Hydrogen bond capacity: None
Impact: Loss of charge, loss of H-bonds, cavity creation

ACMG Classification

Criterion	Strength	Evidence
PM3	Moderate	Detected in trans with pathogenic whole-gene deletion (confirmed paternal)
PP3_Moderate	Moderate	AlphaMissense 0.9016 + REVEL 0.65 concordant (Pejaver 2022 threshold)
PM2_Supporting	Supporting	Absent from gnomAD (0 alleles in 251,000+ individuals)

Result: Likely Pathogenic

2 Moderate + 1 Supporting = Likely Pathogenic per ACMG/AMP 2015 combining rules

Iranfar et al. 2026 - Key Results

PMC12784207 | DOI: 10.1002/ctm2.70571 | Clinical and Translational Medicine, Jan 2026

Vector

Dual AAV9-PHP.eB

STRC cDNA split at nt 2775/2776 (exon 8-9 junction). Both halves within 4.7kb AAV packaging limit.

OHC Transduction

55-64%

Apical 64.2%, medial 55.4%, basal 58.7%. Comparable to wildtype STRC expression.

Hearing Recovery

Near-normal thresholds

DPOAE + ABR restored. Frequency discrimination recovered (Go/No-Go behavioral testing, 100 days post-treatment).

Therapeutic Window

P0-P5 (mice)

After P5, OHC transduction drops below 5%. Authors note: adult treatment may require different AAV serotype.

Gene Therapy Timeline

Dec 2021

Shubina-Oleinik et al. (Science Advances): First dual-AAV STRC gene therapy in mice. Proof of concept. DOI: 10.1126/sciadv.abi7629

Dec 2022

WES performed at HK Children's Hospital. STRC deletion (paternal) + VUS missense (maternal) identified. Lab No: 23C7500174.

Dec 2023

WES report updated with parental testing confirmation. Compound heterozygous STRC.

2025

OTOF gene therapy trials: 11/12 children improved hearing (DB-OTO, NEJM 2025). 3 achieved normal hearing. Precedent for inner ear gene therapy.

Jan 2026

Iranfar et al. (Clinical and Translational Medicine): Dual AAV9-PHP.eB restores hearing to near-normal thresholds in STRC mice. 60% OHC transduction. Frequency discrimination recovered up to 100 days. DOI: 10.1002/ctm2.70571

Mar 2026

AlphaMissense analysis: E1659A scored 0.9016 (Likely Pathogenic). ACMG reclassification evidence: PM3 + PP3_Moderate + PM2_Supporting = Likely Pathogenic.

~2028-29

Expected first-in-human STRC gene therapy trial. Patient will be 7-8 years old. Note: therapeutic window in mice = P0-P5; in humans likely wider but early intervention critical.

Why AlphaMissense Matters for STRC

The STRC Pseudogene Problem

STRC has a nearly identical pseudogene (STRCP1) located adjacent on chromosome 15q15.3. This causes most standard computational tools to fail or return unreliable results for STRC variants:

SIFT

Returns null for E1659A. Cannot reliably align STRC due to pseudogene.

PolyPhen-2

Returns null. Same pseudogene alignment issue.

CADD

No score available for this position. Genomic coordinate mapping affected by pseudogene.

AlphaMissense

Works. Uses protein structure prediction (AlphaFold), not genomic alignment. Immune to pseudogene interference. Score: 0.9016.

AlphaMissense is uniquely valuable for STRC because it predicts pathogenicity from protein structure, bypassing the sequence-alignment step where pseudogene STRCP1 causes other tools to fail. REVEL (0.65) also provides a concordant prediction, using an ensemble approach that partially mitigates this issue.

Active Clinical Trials

No STRC trials yet

As of March 2026, there are no registered clinical trials specifically for STRC/DFNB16 gene therapy. Preclinical evidence (Iranfar 2026, Shubina-Oleinik 2021) supports feasibility. First-in-human trials expected 2028-2029.

Related: Inner Ear Gene Therapy Trials

DB-OTO (Regeneron/Decibel)

AAV gene therapy for OTOF hearing loss. Phase 1/2. 11/12 children improved, 3 achieved normal hearing.

RECRUITING

NCT05788536

OTOV101 (Shanghai/Fudan)

Dual AAV for OTOF hearing loss. Pioneering Chinese trial. First patients treated 2023.

ACTIVE

NCT05901480

Viral Transduction Study (INSERM)

Human auditory sensory cell transduction research. Foundation for future gene therapy vectors.