Is CFAP73 p.Glu26Asp (c.78G>C) pathogenic?

CFAP73 p.Glu26Asp (c.78G>C) is classified Uncertain significance in CFAP73 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-06-07). AlphaMissense: likely benign (0.0952); Very rare (popmax 0.00547%, afr).

How common is CFAP73 p.Glu26Asp (c.78G>C) in the general population?

CFAP73 p.Glu26Asp (c.78G>C) is very rare (popmax 0.00547%, afr) (gnomAD).

What do computational predictors say about CFAP73 p.Glu26Asp (c.78G>C)?

AlphaMissense predicts likely benign (score 0.0952) — an in-silico prediction, not a clinical call.

CFAP73 p.Glu26Asp

c.78G>C · VCV3266521

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0952 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00547%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0952	likely benign
REVEL	0.043	moderately benign-leaning
SaProt	LLR -7.33	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	Δ0.29	acceptor gain · deltas
Constraint at this position
Conservation	phyloP -0.47	GERP -4
Regional constraint	o/e 0.95	unconstrained · MANE · 7,818 bp · p 0.33 · regional, not allelic
Overall
CADD	5.093	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 0.00547% African / African-American · 4/73,166 alleles

Filtering AF 0.00178% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00106%

Overall 0.000357% 5/1,399,254 alleles · very rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00547%	18,292
South Asian	0.00119%	84,040

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: CFAP73
Protein: p.Glu26Asp
Coding: c.78G>C
MANE Select: NM_001144872
Type: single nucleotide variant
Location: chr12:113151939 (GRCh38)
Gene constraint: LOEUF 1.354 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 88.57 · 1 PDB

Full CFAP73 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CFAP73 p.Glu26Gly Uncertain significance ★ ⚠ same residue
DDX54 p.Gly875Asp Uncertain significance ★★ ⚠ same type
CFAP73 p.Ala103Val Uncertain significance ★ ⚠ same type
CFAP73 p.Ala109Gly Uncertain significance ★ ⚠ same type
CFAP73 p.Ala150Glu Uncertain significance ★ ⚠ same type
CFAP73 p.Ala171Thr Uncertain significance ★ ⚠ same type
CFAP73 p.Ala175Val Uncertain significance ★ ⚠ same type
CFAP73 p.Ala186Ser Uncertain significance ★ ⚠ 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/cfap73-p-glu26asp (accessed [today's date]).

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