Is CSAG1 p.Thr12Pro (c.34A>C) pathogenic?

CSAG1 p.Thr12Pro (c.34A>C) is classified Uncertain significance in CSAG1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-05-18). AlphaMissense: likely benign (0.1379); Absent from gnomAD v4.1.

How common is CSAG1 p.Thr12Pro (c.34A>C) in the general population?

CSAG1 p.Thr12Pro (c.34A>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CSAG1 p.Thr12Pro (c.34A>C)?

AlphaMissense predicts likely benign (score 0.1379) — an in-silico prediction, not a clinical call.

CSAG1 p.Thr12Pro

c.34A>C · VCV4007284

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1379 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/2 damaging

AlphaMissense, SaProt

Computational evidence

Protein change
AlphaMissense	0.1379	likely benign
SaProt	LLR -5.23	tolerated
⇒ AlphaMissense and SaProt both call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.62	GERP 1.2
Regional constraint	o/e 1.16	unconstrained · MANE · 4,663 bp · p 0.22 · regional, not allelic
Overall
CADD	4.89	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; SaProt is an independent agreement signal.

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: CSAG1
Protein: p.Thr12Pro
Coding: c.34A>C
MANE Select: NM_001102576
Type: single nucleotide variant
Location: chrX:152728207 (GRCh38)
Structure: AlphaFold pLDDT 63.01

Full CSAG1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CSAG1 p.Ala10Thr Uncertain significance ★ ⚠ same type
CSAG1 p.Ala17Thr Uncertain significance ★ ⚠ same type
CSAG1 p.Ala17Val Uncertain significance ★ ⚠ same type
CSAG1 p.Ala42Ser Uncertain significance ★ ⚠ same type
CSAG1 p.Arg18Gln Uncertain significance ★ ⚠ same type
CSAG1 p.Arg41Pro Uncertain significance ★ same type
CSAG1 p.Arg62Gly Uncertain significance ★ ⚠ same type
CSAG1 p.His50Leu 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/csag1-p-thr12pro (accessed [today's date]).

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