Is ODAPH p.Ile64= (c.192C>T) pathogenic?

ODAPH p.Ile64= (c.192C>T) is classified Uncertain significance in ODAPH (ClinVar, Single submitter, 1 submitter; last evaluated 2021-09-01). Very rare (popmax 0.00329%, sas).

How common is ODAPH p.Ile64= (c.192C>T) in the general population?

ODAPH p.Ile64= (c.192C>T) is very rare (popmax 0.00329%, sas) (gnomAD).

ODAPH p.Ile64=

c.192C>T · rs769319224 · VCV3204030

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00329%, sas)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.014	strongly benign-leaning
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 0.57	GERP 0.2
Overall
CADD	6.344	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00329% South Asian · 3/91,092 alleles

Filtering AF 0.000875% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000443%

Overall 0.000186% 3/1,614,250 alleles · very rare exomes 3/1,461,894 · genomes 0/152,356 · joint denominator

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: ODAPH
Protein: p.Ile64=
Coding: c.192C>T
MANE Select: NM_178497
dbSNP: rs769319224
Type: single nucleotide variant
Location: chr4:75564238 (GRCh38)
Gene constraint: LOEUF 1.704 · pLI 0.07 (gnomAD)
Structure: AlphaFold pLDDT 61.64

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

Similar variants

ODAPH c.67+138A>G Benign ★★ same type
ODAPH c.67+269A>C Benign ★★ same type
ODAPH p.Arg109His Benign ★★ same type
ODAPH p.Pro30Leu Benign ★★ same type
ODAPH p.Ser93Pro Benign ★★ same type
C4orf26 c.318G>A Likely pathogenic ★ same type
ODAPH p.Arg77Ter Pathogenic ★ same type
ODAPH c.67+216A>C Benign ★ same type

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/odaph-p-ile64 (accessed [today's date]).

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