Is RAX p.Asp45= (c.135C>T) pathogenic?

RAX p.Asp45= (c.135C>T) is classified Likely benign in RAX (ClinVar, Single submitter, 1 submitter; last evaluated 2018-05-09). Ultra-rare (popmax 0.0167%, mid).

How common is RAX p.Asp45= (c.135C>T) in the general population?

RAX p.Asp45= (c.135C>T) is ultra-rare (popmax 0.0167%, mid) (gnomAD).

RAX p.Asp45=

c.135C>T · rs1192712648 · VCV742785

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0167%, mid)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.83	GERP -0.22, phastCons 1
Overall
CADD	10.43	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0167% Middle Eastern · 1/5,974 alleles

Overall 6.51e-05% 1/1,535,022 alleles · ultra-rare exomes 1/1,382,724 · genomes 0/152,298 · joint denominator

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: RAX
Protein: p.Asp45=
Coding: c.135C>T
MANE Select: NM_013435
dbSNP: rs1192712648
Type: single nucleotide variant
Location: chr18:59273072 (GRCh38)
Gene constraint: LOEUF 1.197 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 65.10

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

Similar variants

RAX c.*1300A>G Uncertain significance ★★ same type
RAX c.*850C>T Uncertain significance ★★ same type
RAX p.Ala267Val Uncertain significance ★★ ⚠ same type
RAX p.Ala72Gly Uncertain significance ★★ ⚠ same type
RAX p.Arg110Gly Uncertain significance ★★ ⚠ same type
RAX p.Arg166Pro Uncertain significance ★★ ⚠ same type
RAX p.Glu96Gln Uncertain significance ★★ ⚠ same type
RAX p.Gly237Asp 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/rax-p-asp45 (accessed [today's date]).

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