← Home
Part 1

Reclassification Evidence

Computational evidence supporting VUS to Likely Pathogenic reclassification for NM_153700.2:c.4976A>C p.(Glu1659Ala)

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

Evolutionary Conservation

NEW

E1659 is 100% conserved across all tested mammals, spanning ~80 million years of evolution. The surrounding motif PEIFTEIGTIAAG is identical in every species.

Species Position Residue Context
Human1659EPEIFTEIGTIAAG
Mouse1693EPEIFTEIGTIAAG
Rat1693EPEIFTEIGTIAAG
Cow1647EPEIFTEIGTIAAG
Green monkey1659EPEIFTEIGTIAAG
Pig1650EPEIFTEIGTIAAG
Dog1649EPEIFTEIGTIAAG
Bat1646EPEIFTEIGTIAAG
Bear1643EPEIFTEIGTIAAG

9/9 species conserve Glutamic acid (E) at this position. The surrounding 13-residue motif is identical across all tested mammals. This level of conservation strongly suggests functional importance and supports pathogenicity of any substitution (PP1 Supporting evidence per ACMG). Data source: UniProt ortholog sequences, motif-based alignment.

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

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.

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)
PP1_Supporting Supporting E1659 100% conserved across 9 mammalian species (~80M years). Identical motif PEIFTEIGTIAAG.
Result: Likely Pathogenic

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

← Back to overview