Is CTAGE1 p.Pro701Arg (c.2102C>G) pathogenic?

CTAGE1 p.Pro701Arg (c.2102C>G) is classified Likely benign in CTAGE1 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-12-21). AlphaMissense: likely benign (0.0513); Ultra-rare (popmax 0.0286%, sas).

How common is CTAGE1 p.Pro701Arg (c.2102C>G) in the general population?

CTAGE1 p.Pro701Arg (c.2102C>G) is ultra-rare (popmax 0.0286%, sas) (gnomAD).

What do computational predictors say about CTAGE1 p.Pro701Arg (c.2102C>G)?

AlphaMissense predicts likely benign (score 0.0513) — an in-silico prediction, not a clinical call.

CTAGE1 p.Pro701Arg

c.2102C>G · rs548796905 · VCV2217543

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0513 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0286%, sas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0513	likely benign
REVEL	0.183	benign-leaning
SaProt	LLR -6.78	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 -0.9	GERP -3.7
Regional constraint	o/e 1.13	unconstrained · MANE · 2,234 bp · p 0.00025 · regional, not allelic
Overall
CADD	0.036	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 0.0286% South Asian · 26/91,062 alleles

Filtering AF 0.0199% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0171%

Overall 0.00706% 114/1,613,970 alleles · ultra-rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0286%	3,502
Middle Eastern	0.0164%	6,080
Remaining individualsnot grpmax-eligible	0.0128%	7,811
East Asian	0.0111%	8,978
European (non-Finnish)	0.00602%	16,620
Admixed American	0.005%	20,000

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: CTAGE1
Protein: p.Pro701Arg
Coding: c.2102C>G
MANE Select: NM_172241
dbSNP: rs548796905
Type: single nucleotide variant
Location: chr18:22415710 (GRCh38)
Structure: AlphaFold pLDDT 70.45

Full CTAGE1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CTAGE1 p.Ala169= Benign ★★ same type
CTAGE1 p.Ile682Met Benign ★★ same type
CTAGE1 p.Pro686Thr Benign ★★ same type
CTAGE1 p.Val696Met Benign ★★ same type
CTAGE1 p.Ala181Val Uncertain significance ★ ⚠ same type
CTAGE1 p.Ala19Thr Uncertain significance ★ ⚠ same type
CTAGE1 p.Ala282Asp Uncertain significance ★ ⚠ same type
CTAGE1 p.Ala332Thr 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/ctage1-p-pro701arg (accessed [today's date]).

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