Is OTOA p.Pro804Ala (c.2410C>G) pathogenic?

OTOA p.Pro804Ala (c.2410C>G) is classified Uncertain significance in OTOA (ClinVar, Single submitter, 1 submitter; last evaluated 2025-01-02). AlphaMissense: likely benign (0.0718); Very rare (popmax 0.00401%, afr); Associated with Inborn genetic diseases.

What condition is associated with OTOA p.Pro804Ala (c.2410C>G)?

OTOA p.Pro804Ala (c.2410C>G) is associated with Inborn genetic diseases (ClinVar).

How common is OTOA p.Pro804Ala (c.2410C>G) in the general population?

OTOA p.Pro804Ala (c.2410C>G) is very rare (popmax 0.00401%, afr) (gnomAD).

What do computational predictors say about OTOA p.Pro804Ala (c.2410C>G)?

AlphaMissense predicts likely benign (score 0.0718) — an in-silico prediction, not a clinical call.

OTOA p.Pro804Ala

c.2410C>G · VCV3884655

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0718 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00401%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.0718	likely benign
REVEL	0.066	moderately benign-leaning
SaProt	LLR -6.96	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Regional constraint	o/e 0.96	unconstrained · MANE · 21 kb · p 0.73 · regional, not allelic
Overall
CADD	1.73	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

⚠ Isoform check: AlphaMissense numbered on a different transcript (AM P818A vs ClinVar P804A) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00401% African / African-American · 3/74,882 alleles

Filtering AF 0.00275% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00244%

Overall 0.00285% 46/1,613,972 alleles · very rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00401%	24,961
European (non-Finnish)	0.00364%	27,442

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: OTOA
Protein: p.Pro804Ala
Coding: c.2410C>G
MANE Select: NM_144672
Type: single nucleotide variant
Location: chr16:21736369 (GRCh38)
Gene constraint: LOEUF 0.822 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 84.12

Full OTOA gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

OTOA p.Ala364Thr Uncertain significance ★★ ⚠ same condition
OTOA p.Ala40Val Uncertain significance ★★ ⚠ same condition
OTOA p.Ala477Pro Uncertain significance ★★ ⚠ same condition
OTOA p.Arg1027Trp Uncertain significance ★★ ⚠ same condition
OTOA p.Arg202Pro Uncertain significance ★★ ⚠ same condition
OTOA p.Arg29Lys Uncertain significance ★★ ⚠ same condition
OTOA p.Arg475Lys Uncertain significance ★★ ⚠ same condition
OTOA p.Arg797Trp Uncertain significance ★★ ⚠ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/otoa-p-pro804ala (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown