Is COCH p.Asn64Ser (c.191A>G) pathogenic?

COCH p.Asn64Ser (c.191A>G) is classified Uncertain significance in COCH (ClinVar, Single submitter, 1 submitter; last evaluated 2024-06-07). AlphaMissense: likely benign (0.0922); Very rare (popmax 0.000254%, nfe); Associated with Inborn genetic diseases.

What condition is associated with COCH p.Asn64Ser (c.191A>G)?

COCH p.Asn64Ser (c.191A>G) is associated with Inborn genetic diseases (ClinVar).

How common is COCH p.Asn64Ser (c.191A>G) in the general population?

COCH p.Asn64Ser (c.191A>G) is very rare (popmax 0.000254%, nfe) (gnomAD).

What do computational predictors say about COCH p.Asn64Ser (c.191A>G)?

AlphaMissense predicts likely benign (score 0.0922) — an in-silico prediction, not a clinical call.

COCH p.Asn64Ser

c.191A>G · VCV3268446

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0922 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.000254%, nfe)

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.0922	likely benign
REVEL	0.294	indeterminate
SaProt	LLR -3.92	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 11	GERP 1.8, phastCons 1
Regional constraint	o/e 0.90	unconstrained · MANE · 15 kb · p 0.0071 · regional, not allelic
Overall
CADD	20.3	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.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000254% European (non-Finnish) · 3/1,180,040 alleles

Filtering AF 6.8e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.9e-05%

Overall 0.000274% 4/1,461,892 alleles · very rare

Ancestry group	Frequency	1 in
Remaining individualsnot grpmax-eligible	0.0016%	62,512
European (non-Finnish)grpmax	0.000254%	393,346

Remaining individuals shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: COCH
Protein: p.Asn64Ser
Coding: c.191A>G
MANE Select: NM_004086
Type: single nucleotide variant
Location: chr14:30877680 (GRCh38)
Gene constraint: LOEUF 0.896 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 85.93 · 1 PDB
Residue 64: a disulfide bond; the lccl domain; a β-strand

Full COCH 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

COCH p.Arg148Gln Uncertain significance ★★ ⚠ same condition
COCH p.Asn335Ser Uncertain significance ★★ ⚠ same condition
COCH p.Glu25Gln Uncertain significance ★★ ⚠ same condition
COCH p.Gly135Arg Uncertain significance ★★ ⚠ same condition
COCH p.Gly327Ser Uncertain significance ★★ ⚠ same condition
COCH p.Gly75Glu Uncertain significance ★★ ⚠ same condition
COCH p.Met194Ile Uncertain significance ★★ ⚠ same condition
COCH p.Phe255Ser 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/coch-p-asn64ser (accessed [today's date]).

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