Is CFAP43 p.Arg938Gln (c.2813G>A) pathogenic?

CFAP43 p.Arg938Gln (c.2813G>A) is classified Uncertain significance in CFAP43 (ClinVar, Single submitter, 2 submitters; last evaluated 2021-07-26). AlphaMissense: likely benign (0.0657); Ultra-rare (popmax 0.031%, afr).

How common is CFAP43 p.Arg938Gln (c.2813G>A) in the general population?

CFAP43 p.Arg938Gln (c.2813G>A) is ultra-rare (popmax 0.031%, afr) (gnomAD).

What do computational predictors say about CFAP43 p.Arg938Gln (c.2813G>A)?

AlphaMissense predicts likely benign (score 0.0657) — an in-silico prediction, not a clinical call.

CFAP43 p.Arg938Gln

c.2813G>A · rs199794656 · VCV2354390

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.0657 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.031%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0657	likely benign
REVEL	0.061	moderately benign-leaning
SaProt	LLR -5.11	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.021	GERP 0.22, phastCons 0.001
Regional constraint	o/e 0.92	unconstrained · MANE · 91 kb · p 0.0013 · regional, not allelic
Overall
CADD	17.54	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 0.031% African / African-American · 23/74,306 alleles

Filtering AF 0.0211% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0179%

Overall 0.00819% 131/1,599,768 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.031%	3,231
Admixed American	0.0278%	3,600
Middle Eastern	0.0166%	6,012
Remaining individualsnot grpmax-eligible	0.00808%	12,379
European (non-Finnish)	0.0069%	14,483
South Asian	0.00452%	22,142
Ashkenazi Jewishnot grpmax-eligible	0.00345%	28,994

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: CFAP43
Protein: p.Arg938Gln
Coding: c.2813G>A
MANE Select: NM_025145
dbSNP: rs199794656
Type: single nucleotide variant
Location: chr10:104166714 (GRCh38)
Gene constraint: LOEUF 0.78 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 77.27 · 1 PDB
Residue 938: a UniProt-annotated variant site (in spgf19)

Full CFAP43 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CFAP43 p.Arg894Ter Pathogenic/Likely pathogenic ★★ same type
CFAP43 p.Thr1075Lys Uncertain significance ★★ ⚠ same type
CFAP43 c.2142-4A>G Benign ★★ same type
CFAP43 p.Glu1540Gly Benign/Likely benign ★★ same type
CFAP43 p.Leu1542Val Benign/Likely benign ★★ same type
CFAP43 p.Leu616Phe Benign ★★ ⚠ same type
CFAP43 p.Leu802= Benign ★★ same type
CFAP43 p.Pro246= 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/cfap43-p-arg938gln (accessed [today's date]).

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