Is CSPG5 p.Phe213= (c.639C>T) pathogenic?

CSPG5 p.Phe213= (c.639C>T) is classified Likely benign in CSPG5 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-07-01). Very rare (popmax 0.000424%, nfe).

How common is CSPG5 p.Phe213= (c.639C>T) in the general population?

CSPG5 p.Phe213= (c.639C>T) is very rare (popmax 0.000424%, nfe) (gnomAD).

CSPG5 p.Phe213=

c.639C>T · rs746592573 · VCV2653765

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.000424%, nfe)

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 -1.8	GERP -3
Overall
CADD	8.55	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000424% European (non-Finnish) · 5/1,180,016 alleles

Filtering AF 0.000124% ClinGen BA1/BS1 input FAF95, joint · FAF99 9e-05%

Overall 0.000342% 5/1,461,882 alleles · very rare

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: CSPG5
Protein: p.Phe213=
Coding: c.639C>T
MANE Select: NM_006574
dbSNP: rs746592573
Type: single nucleotide variant
Location: chr3:47577387 (GRCh38)
Gene constraint: LOEUF 0.897 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 52.52

Full CSPG5 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CSPG5 p.Thr126= Benign ★★ same type
CSPG5 c.1458+20C>A Uncertain significance ★ ⚠ same type
CSPG5 c.1458+26G>T Uncertain significance ★ ⚠ same type
CSPG5 c.1458+38C>T Uncertain significance ★ ⚠ same type
CSPG5 c.1458+40C>T Uncertain significance ★ ⚠ same type
CSPG5 c.1458+46C>T Uncertain significance ★ ⚠ same type
CSPG5 c.1458+62A>C Uncertain significance ★ ⚠ same type
CSPG5 c.1458+62A>G 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/cspg5-p-phe213 (accessed [today's date]).

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