Is CSF2 p.Ala13Thr (c.37G>A) pathogenic?

CSF2 p.Ala13Thr (c.37G>A) is classified Uncertain significance in CSF2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-09-22). AlphaMissense: likely benign (0.1254); Absent from gnomAD v4.1.

How common is CSF2 p.Ala13Thr (c.37G>A) in the general population?

CSF2 p.Ala13Thr (c.37G>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CSF2 p.Ala13Thr (c.37G>A)?

AlphaMissense predicts likely benign (score 0.1254) — an in-silico prediction, not a clinical call.

CSF2 p.Ala13Thr

c.37G>A · VCV4656962

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1254 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1254	likely benign
REVEL	0.099	moderately benign-leaning
SaProt	LLR -7.15	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 9.2	GERP 2.6, phastCons 1
Regional constraint	o/e 0.78	unconstrained · MANE · 2,025 bp · p 0.0039 · regional, not allelic
Overall
CADD	24.1	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; 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: CSF2
Protein: p.Ala13Thr
Coding: c.37G>A
MANE Select: NM_000758
Type: single nucleotide variant
Location: chr5:132073860 (GRCh38)
Gene constraint: LOEUF 0.619 · pLI 0.85 (gnomAD)
Structure: AlphaFold pLDDT 88.30 · 11 PDB

Full CSF2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CSF2 p.Thr115Ile Likely benign ★★ same type
CSF2 p.Arg21Cys Uncertain significance ★ ⚠ same type
CSF2 p.Arg41His Uncertain significance ★ ⚠ same type
CSF2 p.Arg84Pro Uncertain significance ★ ⚠ same type
CSF2 p.Glu52Asp Uncertain significance ★ ⚠ same type
CSF2 p.Leu127Met Uncertain significance ★ ⚠ same type
CSF2 p.Met53Thr Uncertain significance ★ ⚠ same type
CSF2 p.Phe136Leu 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/csf2-p-ala13thr (accessed [today's date]).

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