Is RAX p.Pro288Ser (c.862C>T) pathogenic?

RAX p.Pro288Ser (c.862C>T) is classified Uncertain significance in RAX (ClinVar, Single submitter, 1 submitter; last evaluated 2024-01-16). AlphaMissense: likely benign (0.0599); No allele count reported in gnomAD v4.1 (AN 1,552,836); Associated with Inborn genetic diseases.

What condition is associated with RAX p.Pro288Ser (c.862C>T)?

RAX p.Pro288Ser (c.862C>T) is associated with Inborn genetic diseases (ClinVar).

How common is RAX p.Pro288Ser (c.862C>T) in the general population?

RAX p.Pro288Ser (c.862C>T) is no allele count reported in gnomAD v4.1 (AN 1,552,836) (gnomAD).

What do computational predictors say about RAX p.Pro288Ser (c.862C>T)?

AlphaMissense predicts likely benign (score 0.0599) — an in-silico prediction, not a clinical call.

RAX p.Pro288Ser

c.862C>T · rs2511486988 · VCV3152015

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0599 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,552,836)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.0599	likely benign
REVEL	0.218	benign-leaning
SaProt	LLR -11.02	damaging
⇒ SaProt calls this damaging; AlphaMissense and REVEL do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 3.1	GERP 1.7, phastCons 1
Regional constraint	o/e 1.05	unconstrained · MANE · 4,199 bp · p 0.25 · regional, not allelic
Overall
CADD	16.49	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

No allele count reported in gnomAD v4.1 (AN 1,552,836). 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: RAX
Protein: p.Pro288Ser
Coding: c.862C>T
MANE Select: NM_013435
dbSNP: rs2511486988
Type: single nucleotide variant
Location: chr18:59269183 (GRCh38)
Gene constraint: LOEUF 1.197 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 65.10
Residue 288: the 'disordered' region

Full RAX 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

RAX p.Pro288Gln Uncertain significance ★★ ⚠ same residue
RAX p.Ala267Val Uncertain significance ★★ ⚠ same condition
RAX p.Ala72Gly Uncertain significance ★★ ⚠ same condition
RAX p.Arg166Pro Uncertain significance ★★ ⚠ same condition
RAX p.Glu96Gln Uncertain significance ★★ ⚠ same condition
RAX p.Leu289Phe Uncertain significance ★★ ⚠ same condition
RAX p.Lys333Arg Uncertain significance ★★ ⚠ same condition
RAX p.Phe51Leu 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/rax-p-pro288ser (accessed [today's date]).

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