Is CSTA p.Lys30Asn (c.90A>T) pathogenic?

CSTA p.Lys30Asn (c.90A>T) is classified Uncertain significance in CSTA (ClinVar, Single submitter, 1 submitter; last evaluated 2025-02-25). AlphaMissense: likely benign (0.2791); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with CSTA p.Lys30Asn (c.90A>T)?

CSTA p.Lys30Asn (c.90A>T) is associated with Inborn genetic diseases (ClinVar).

How common is CSTA p.Lys30Asn (c.90A>T) in the general population?

CSTA p.Lys30Asn (c.90A>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CSTA p.Lys30Asn (c.90A>T)?

AlphaMissense predicts likely benign (score 0.2791) — an in-silico prediction, not a clinical call.

CSTA p.Lys30Asn

c.90A>T · VCV3836995

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2791 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.2791	likely benign
REVEL	0.127	moderately benign-leaning
SaProt	LLR -12.18	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 5.8	GERP 1.8, phastCons 1
Regional constraint	o/e 1.04	unconstrained · MANE · 16 kb · p 0.65 · regional, not allelic
Overall
CADD	22.2	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

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: CSTA
Protein: p.Lys30Asn
Coding: c.90A>T
MANE Select: NM_005213
Type: single nucleotide variant
Location: chr3:122337570 (GRCh38)
Gene constraint: LOEUF 1.219 · pLI 0.12 (gnomAD)
Structure: AlphaFold pLDDT 93.57 · 14 PDB
Residue 30: 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.Gln17Arg Uncertain significance ★ ⚠ same condition
CSTA p.Gln42Arg Uncertain significance ★ ⚠ same condition
CSTA p.Glu94Lys 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-lys30asn (accessed [today's date]).

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