Is CSTA p.Gln17Arg (c.50A>G) pathogenic?

CSTA p.Gln17Arg (c.50A>G) is classified Uncertain significance in CSTA (ClinVar, Single submitter, 1 submitter; last evaluated 2024-03-16). AlphaMissense: likely benign (0.222); Very rare (popmax 0.00534%, afr); Associated with Inborn genetic diseases.

What condition is associated with CSTA p.Gln17Arg (c.50A>G)?

CSTA p.Gln17Arg (c.50A>G) is associated with Inborn genetic diseases (ClinVar).

How common is CSTA p.Gln17Arg (c.50A>G) in the general population?

CSTA p.Gln17Arg (c.50A>G) is very rare (popmax 0.00534%, afr) (gnomAD).

What do computational predictors say about CSTA p.Gln17Arg (c.50A>G)?

AlphaMissense predicts likely benign (score 0.222) — an in-silico prediction, not a clinical call.

CSTA p.Gln17Arg

c.50A>G · VCV3269968

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.222 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00534%, afr)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.222	likely benign
REVEL	0.112	moderately benign-leaning
SaProt	LLR -11.15	damaging
⇒ SaProt calls this damaging; AlphaMissense and REVEL do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 11	GERP 2.1, phastCons 1
Regional constraint	o/e 1.04	unconstrained · MANE · 16 kb · p 0.65 · regional, not allelic
Overall
CADD	26.1	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 0.00534% African / African-American · 4/74,938 alleles

Filtering AF 0.00239% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0021%

Overall 0.00279% 45/1,614,052 alleles · very rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00534%	18,734
Admixed American	0.00333%	30,000
European (non-Finnish)	0.00322%	31,053
Remaining individualsnot grpmax-eligible	0.0016%	62,486

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: CSTA
Protein: p.Gln17Arg
Coding: c.50A>G
MANE Select: NM_005213
Type: single nucleotide variant
Location: chr3:122325342 (GRCh38)
Gene constraint: LOEUF 1.219 · pLI 0.12 (gnomAD)
Structure: AlphaFold pLDDT 93.57 · 14 PDB
Residue 17: an α-helix

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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CSTA p.Ala12Thr Uncertain significance ★ ⚠ same condition
CSTA p.Arg58Gln Uncertain significance ★ ⚠ same condition
CSTA p.Arg58Pro Uncertain significance ★ ⚠ same condition
CSTA p.Asp92Val Uncertain significance ★ ⚠ same condition
CSTA p.Gln42Arg Uncertain significance ★ ⚠ same condition
CSTA p.Glu94Lys Uncertain significance ★ ⚠ same condition
CSTA p.Lys30Asn Uncertain significance ★ ⚠ same condition
CSTA p.Lys63Thr Uncertain significance ★ ⚠ same condition

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/csta-p-gln17arg (accessed [today's date]).

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