Is CRMP1 p.Pro466= (c.1398C>G) pathogenic?

CRMP1 p.Pro466= (c.1398C>G) is classified Benign in CRMP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2018-01-12). Rare (popmax 0.24%, amr).

How common is CRMP1 p.Pro466= (c.1398C>G) in the general population?

CRMP1 p.Pro466= (c.1398C>G) is rare (popmax 0.24%, amr) (gnomAD).

CRMP1 p.Pro466=

c.1398C>G · rs548053386 · VCV732507

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.24%, amr)

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 -8	GERP -4.4
Overall
CADD	0.552	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.24% Admixed American · 144/60,018 alleles

Filtering AF 0.208% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.196%

Overall 0.00898% 145/1,613,990 alleles · rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.24%	417
East Asian	0.00223%	44,874

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: CRMP1
Protein: p.Pro466=
Coding: c.1398C>G
MANE Select: NM_001014809
dbSNP: rs548053386
Type: single nucleotide variant
Location: chr4:5836819 (GRCh38)
Gene constraint: LOEUF 0.44 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 90.46 · 1 PDB

Full CRMP1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CRMP1 c.820+8A>G Benign ★★ same type
CRMP1 c.964-8T>C Benign ★★ same type
CRMP1 p.Ala357= Benign ★★ same type
CRMP1 p.Gly261Arg Benign ★★ same type
CRMP1 p.Val524= Benign ★★ same type
CRMP1 c.381+2933T>C Uncertain significance ★ same type
CRMP1 p.Ala174Val Uncertain significance ★ ⚠ same type
CRMP1 p.Ala199Ser 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/crmp1-p-pro466 (accessed [today's date]).

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