Is CFAP73 p.Lys233Arg (c.698A>G) pathogenic?

CFAP73 p.Lys233Arg (c.698A>G) is classified Uncertain significance in CFAP73 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-07-16). AlphaMissense: likely benign (0.0845); Rare (popmax 0.184%, afr).

How common is CFAP73 p.Lys233Arg (c.698A>G) in the general population?

CFAP73 p.Lys233Arg (c.698A>G) is rare (popmax 0.184%, afr) (gnomAD).

What do computational predictors say about CFAP73 p.Lys233Arg (c.698A>G)?

AlphaMissense predicts likely benign (score 0.0845) — an in-silico prediction, not a clinical call.

CFAP73 p.Lys233Arg

c.698A>G · rs747866706 · VCV3143656

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0845 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.184%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0845	likely benign
REVEL	0.052	moderately benign-leaning
SaProt	LLR -4.87	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · A>T here scores Δ0.21 · evaluated, not missing
Constraint at this position
Conservation	phyloP -0.26	GERP -2.8
Regional constraint	o/e 0.95	unconstrained · MANE · 7,818 bp · p 0.33 · regional, not allelic
Overall
CADD	17.92	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 0.184% African / African-American · 134/72,716 alleles

Filtering AF 0.159% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.149%

Overall 0.0101% 154/1,531,878 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.184%	543
Remaining individualsnot grpmax-eligible	0.0186%	5,374
Admixed American	0.00793%	12,609
South Asian	0.00241%	41,562
European (non-Finnish)	0.000265%	377,121

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.Lys233Arg
Coding: c.698A>G
MANE Select: NM_001144872
dbSNP: rs747866706
Type: single nucleotide variant
Location: chr12:113155267 (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

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
CFAP73 p.Ala214Thr 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-lys233arg (accessed [today's date]).

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