Is GPC6 p.Pro522= (c.1566C>T) pathogenic?

GPC6 p.Pro522= (c.1566C>T) is classified Uncertain significance in GPC6 (ClinVar, Single submitter, 1 submitter; last evaluated 2018-01-12). Very rare (popmax 0.00668%, eas); Associated with autosomal recessive omodysplasia.

What condition is associated with GPC6 p.Pro522= (c.1566C>T)?

GPC6 p.Pro522= (c.1566C>T) is associated with autosomal recessive omodysplasia (ClinVar).

How common is GPC6 p.Pro522= (c.1566C>T) in the general population?

GPC6 p.Pro522= (c.1566C>T) is very rare (popmax 0.00668%, eas) (gnomAD).

GPC6 p.Pro522=

c.1566C>T · rs1278326769 · VCV882732

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00668%, eas)

Conditions

autosomal recessive omodysplasia

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 -9.6	GERP -4.5
Overall
CADD	3.44	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00668% East Asian · 3/44,888 alleles

Filtering AF 0.00177% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000891%

Overall 0.00123% 18/1,461,382 alleles · very rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00668%	14,963
African / African-American	0.00133%	75,040
European (non-Finnish)	0.0011%	90,737
South Asian	0.0011%	91,072

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: GPC6
Protein: p.Pro522=
Coding: c.1566C>T
MANE Select: NM_005708
dbSNP: rs1278326769
Type: single nucleotide variant
Location: chr13:94403115 (GRCh38)
Gene constraint: LOEUF 0.384 · pLI 1.00 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 82.67

Full GPC6 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

autosomal recessive omodysplasia — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

GPC6 p.Pro522Ser Uncertain significance ★ ⚠ same residue
GPC6 p.Arg171Trp Pathogenic/Likely pathogenic ★★ same condition
GPC6 p.Ala377Thr Uncertain significance ★★ ⚠ same condition
GPC6 p.Arg363His Uncertain significance ★★ same condition
GPC6 p.Arg524Trp Uncertain significance ★★ ⚠ same condition
GPC6 p.Arg534His Uncertain significance ★★ ⚠ same condition
GPC6 p.Ile388Val Uncertain significance ★★ ⚠ same condition
GPC6 p.Ile406Val 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/gpc6-p-pro522 (accessed [today's date]).

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