Is ROBO2 p.Arg7Ser (c.19C>A) pathogenic?

ROBO2 p.Arg7Ser (c.19C>A) is classified Benign in ROBO2 (ClinVar, Single submitter, 3 submitters; last evaluated 2016-02-15). No allele count reported in gnomAD v4.1 (AN 1,571,706); Associated with vesicoureteral reflux 2.

What condition is associated with ROBO2 p.Arg7Ser (c.19C>A)?

ROBO2 p.Arg7Ser (c.19C>A) is associated with vesicoureteral reflux 2 (ClinVar).

How common is ROBO2 p.Arg7Ser (c.19C>A) in the general population?

ROBO2 p.Arg7Ser (c.19C>A) is no allele count reported in gnomAD v4.1 (AN 1,571,706) (gnomAD).

ROBO2 p.Arg7Ser

c.19C>A · rs12171318 · VCV518348

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 3 submitters

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,571,706)

Conditions

vesicoureteral reflux 2

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.014	strongly benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.4	GERP -2.8, phastCons 0.019
Overall
CADD	0.236	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,571,706). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: ROBO2
Protein: p.Arg7Ser
Coding: c.19C>A
MANE Select: NM_001395656 · reported on NM_001128929
dbSNP: rs12171318
Type: single nucleotide variant
Location: chr3:75937512 (GRCh38)
Gene constraint: LOEUF 0.412 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 67.78 · 6 PDB

Full ROBO2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

vesicoureteral reflux 2 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

ROBO2 c.1244-1G>A Uncertain significance ★★ same condition
ROBO2 c.3148+2T>C Uncertain significance ★★ same condition
ROBO2 p.Ala112Gly Uncertain significance ★★ same condition
ROBO2 p.Ala124= Uncertain significance ★★ same condition
ROBO2 p.Ala124Val Uncertain significance ★★ same condition
ROBO2 p.Ala556Thr Uncertain significance ★★ ⚠ same condition
ROBO2 p.Ala824Val Uncertain significance ★★ ⚠ same condition
ROBO2 p.Ala872Gly 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/robo2-p-arg7ser (accessed [today's date]).

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