Is ROR2 p.Gln532= (c.1596A>G) pathogenic?

ROR2 p.Gln532= (c.1596A>G) is classified Conflicting classifications of pathogenicity in ROR2 (ClinVar, Conflicting submitters, 2 submitters; last evaluated 2025-10-07). Rare (popmax 0.423%, eas); Associated with brachydactyly type B1.

What condition is associated with ROR2 p.Gln532= (c.1596A>G)?

ROR2 p.Gln532= (c.1596A>G) is associated with brachydactyly type B1, autosomal recessive Robinow syndrome (ClinVar).

How common is ROR2 p.Gln532= (c.1596A>G) in the general population?

ROR2 p.Gln532= (c.1596A>G) is rare (popmax 0.423%, eas) (gnomAD).

ROR2 p.Gln532=

c.1596A>G · rs528393492 · VCV913252

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

rare (popmax 0.423%, eas)

Conditions

brachydactyly type B1

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 -0.49, phastCons 1
Overall
CADD	10.11	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.423% East Asian · 189/44,704 alleles

Filtering AF 0.373% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.354%

Overall 0.0142% 229/1,607,112 alleles · rare exomes 215/1,454,830 · genomes 14/152,282 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.423%	237
South Asian	0.032%	3,126
African / African-American	0.00668%	14,981
Admixed American	0.00501%	19,949
Remaining individualsnot grpmax-eligible	0.00483%	20,717

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: ROR2
Protein: p.Gln532=
Coding: c.1596A>G
MANE Select: NM_004560
dbSNP: rs528393492
Type: single nucleotide variant
Location: chr9:91724898 (GRCh38)
Gene constraint: LOEUF 0.543 · pLI 0.35 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 69.09 · 6 PDB
Residue 532: the protein kinase domain

Full ROR2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

brachydactyly type B1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: autosomal recessive Robinow syndrome

Similar variants

ROR2 c.175+1G>A Likely pathogenic ★★ same condition
ROR2 p.Arg119Ter Pathogenic ★★ same condition
ROR2 p.Arg397Ter Pathogenic ★★ same condition
ROR2 p.Arg442Ter Pathogenic ★★ same condition
ROR2 p.Arg528Ter Pathogenic/Likely pathogenic ★★ same condition
ROR2 c.175+3G>T Uncertain significance ★★ same condition
ROR2 c.-102G>T Uncertain significance ★★ same condition
ROR2 c.*135G>T 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/ror2-p-gln532 (accessed [today's date]).

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