Is CSF2RB p.Glu627fs (c.1879del) pathogenic?

CSF2RB p.Glu627fs (c.1879del) is classified Uncertain significance in CSF2RB (ClinVar, Single submitter, 1 submitter; last evaluated 2022-10-20). No gnomAD frequency available for this variant.

How common is CSF2RB p.Glu627fs (c.1879del) in the general population?

CSF2RB p.Glu627fs (c.1879del) is no gnomAD frequency available for this variant (gnomAD).

CSF2RB p.Glu627fs

c.1879del · rs2518008924 · VCV2036357

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a LoF-intolerant gene
NMD	escapes	premature termination codon in the last exon (14 of 14) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 4.7	GERP 1.5, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: CSF2RB
Protein: p.Glu627fs
Coding: c.1879del
MANE Select: NM_000395
dbSNP: rs2518008924
Type: Deletion
Location: chr22:36937686 (GRCh38)
Gene constraint: LOEUF 0.511 · pLI 0.93 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 65.50 · 10 PDB
Residue 627: the 'disordered' region

Full CSF2RB gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CSF2RB p.Glu627Gly Uncertain significance ★ ⚠ same residue
CSF2RB p.Trp152fs Uncertain significance ★★ same type
CSF2RB p.Ala662fs Uncertain significance ★ same type
CSF2RB p.Cys16fs Uncertain significance ★ same type
CSF2RB p.Cys745fs Uncertain significance ★ same type
CSF2RB p.Gln194fs Uncertain significance ★ same type
CSF2RB p.Gln660fs Uncertain significance ★ same type
CSF2RB p.Gln856fs 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/csf2rb-p-glu627fs (accessed [today's date]).

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