Is CSF1R p.Glu949Lys (c.2845G>A) pathogenic?

CSF1R p.Glu949Lys (c.2845G>A) is classified Uncertain significance in CSF1R (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-23). AlphaMissense: likely benign (0.0824); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with CSF1R p.Glu949Lys (c.2845G>A)?

CSF1R p.Glu949Lys (c.2845G>A) is associated with Inborn genetic diseases (ClinVar).

How common is CSF1R p.Glu949Lys (c.2845G>A) in the general population?

CSF1R p.Glu949Lys (c.2845G>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CSF1R p.Glu949Lys (c.2845G>A)?

AlphaMissense predicts likely benign (score 0.0824) — an in-silico prediction, not a clinical call.

CSF1R p.Glu949Lys

c.2845G>A · VCV4234819

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0824 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.0824	likely benign
REVEL	0.182	moderately benign-leaning
SaProt	LLR -8.03	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Pangolin	Δ0.21	gain · loss 0.00 · not in the SpliceAI release · independent
Constraint at this position
Conservation	phyloP 3.9	GERP 2, phastCons 1
Regional constraint	o/e 1.08	unconstrained · MANE · 279 bp · p 0.48 · regional, not allelic
Overall
CADD	22.3	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: CSF1R
Protein: p.Glu949Lys
Coding: c.2845G>A
MANE Select: NM_001288705
Type: single nucleotide variant
Location: chr5:150054143 (GRCh38)
Gene constraint: LOEUF 0.485 · pLI 0.98 (gnomAD)
Structure: AlphaFold pLDDT 78.08 · 26 PDB
Residue 949: the 'disordered' region; a UniProt-annotated variant site (in banddos)

Full CSF1R 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

CSF1R p.Glu949= Likely benign ★★ same residue
CSF1R p.Ala299Val Uncertain significance ★★ ⚠ same condition
CSF1R p.Ala770Thr Uncertain significance ★★ ⚠ same condition
CSF1R p.Arg41Gln Uncertain significance ★★ ⚠ same condition
CSF1R p.Arg549Cys Uncertain significance ★★ ⚠ same condition
CSF1R p.Arg710Cys Uncertain significance ★★ ⚠ same condition
CSF1R p.Gln173Arg Uncertain significance ★★ ⚠ same condition
CSF1R p.Glu628Ala 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/csf1r-p-glu949lys (accessed [today's date]).

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