Is CFP p.Arg79Gln (c.236G>A) pathogenic?

CFP p.Arg79Gln (c.236G>A) is classified Benign/Likely benign in CFP (ClinVar, Multiple submitters, 4 submitters; last evaluated 2025-12-15). AlphaMissense: likely benign (0.0644); Rare (popmax 0.973%, sas).

How common is CFP p.Arg79Gln (c.236G>A) in the general population?

CFP p.Arg79Gln (c.236G>A) is rare (popmax 0.973%, sas) (gnomAD).

What do computational predictors say about CFP p.Arg79Gln (c.236G>A)?

AlphaMissense predicts likely benign (score 0.0644) — an in-silico prediction, not a clinical call.

CFP p.Arg79Gln

c.236G>A · rs761962858 · VCV235395

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

AlphaMissense

likely benign

0.0644 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.973%, sas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0644	likely benign
REVEL	0.027	moderately benign-leaning
SaProt	LLR -5.34	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 -8.4	GERP -3.5
Regional constraint	o/e 0.79	unconstrained · MANE · 5,566 bp · p 3.9e-05 · regional, not allelic
Overall
CADD	0.008	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.973% South Asian · 547/56,193 alleles

Filtering AF 0.906% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.879%

Overall 0.0553% 667/1,206,119 alleles · rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.973%	103
Remaining individualsnot grpmax-eligible	0.0695%	1,438
Middle Eastern	0.0689%	1,450
East Asian	0.0119%	8,400
European (non-Finnish)	0.00885%	11,305
African / African-American	0.00175%	57,081

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: CFP
Protein: p.Arg79Gln
Coding: c.236G>A
MANE Select: NM_001145252
dbSNP: rs761962858
Type: single nucleotide variant
Location: chrX:47628269 (GRCh38)
Structure: AlphaFold pLDDT 83.75 · 14 PDB
Residue 79: the tsp type-1 1 domain

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

Similar variants

CFP p.Trp321Gly Pathogenic ★★ same type
CFP p.Ala402Gly Uncertain significance ★★ ⚠ same type
CFP p.Arg157Gln Uncertain significance ★★ ⚠ same type
CFP p.Arg157Trp Uncertain significance ★★ ⚠ same type
CFP p.Arg159Cys Uncertain significance ★★ ⚠ same type
CFP p.Arg247Trp Uncertain significance ★★ ⚠ same type
CFP p.Arg438Trp Uncertain significance ★★ ⚠ same type
CFP p.Asn307Ser 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/cfp-p-arg79gln (accessed [today's date]).

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