Is CSF2RB p.Ser20Arg (c.60C>A) pathogenic?

CSF2RB p.Ser20Arg (c.60C>A) is classified Benign/Likely benign in CSF2RB (ClinVar, Multiple submitters, 3 submitters; last evaluated 2026-02-02). AlphaMissense: likely benign (0.2067); Rare (popmax 0.892%, eas).

How common is CSF2RB p.Ser20Arg (c.60C>A) in the general population?

CSF2RB p.Ser20Arg (c.60C>A) is rare (popmax 0.892%, eas) (gnomAD).

What do computational predictors say about CSF2RB p.Ser20Arg (c.60C>A)?

AlphaMissense predicts likely benign (score 0.2067) — an in-silico prediction, not a clinical call.

CSF2RB p.Ser20Arg

c.60C>A · rs200588212 · VCV1168184

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

AlphaMissense

likely benign

0.2067 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.892%, eas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.2067	likely benign
REVEL	0.157	moderately benign-leaning
SaProt	LLR -7.80	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 -7.9	GERP -3.2
Regional constraint	o/e 0.85	unconstrained · MANE · 14 kb · p 0.00014 · regional, not allelic
Overall
CADD	0.02	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

Grpmax group 0.892% East Asian · 386/43,252 alleles

Filtering AF 0.819% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.79%

Overall 0.0296% 467/1,578,894 alleles · rare exomes 412/1,426,626 · genomes 55/152,268 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.892%	112
Remaining individualsnot grpmax-eligible	0.0622%	1,608
South Asian	0.00696%	14,365
Admixed American	0.00362%	27,619
European (non-Finnish)	0.00292%	34,194
Finnishnot grpmax-eligible	0.00163%	61,448

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: CSF2RB
Protein: p.Ser20Arg
Coding: c.60C>A
MANE Select: NM_000395
dbSNP: rs200588212
Type: single nucleotide variant
Location: chr22:36922267 (GRCh38)
Gene constraint: LOEUF 0.511 · pLI 0.93 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 65.50 · 10 PDB

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

Similar variants

CSF2RB p.Ala185Thr Uncertain significance ★★ ⚠ same type
CSF2RB p.Ala255Thr Uncertain significance ★★ ⚠ same type
CSF2RB p.Ala314Thr Uncertain significance ★★ ⚠ same type
CSF2RB p.Ala314Val Uncertain significance ★★ ⚠ same type
CSF2RB p.Ala394Thr Uncertain significance ★★ ⚠ same type
CSF2RB p.Ala455Thr Uncertain significance ★★ ⚠ same type
CSF2RB p.Ala576Thr Uncertain significance ★★ ⚠ same type
CSF2RB p.Ala662Thr 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-ser20arg (accessed [today's date]).

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