Is RBP1 p.Arg9= (c.27C>G) pathogenic?

RBP1 p.Arg9= (c.27C>G) is classified Likely benign in RBP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-10-04). Rare (popmax 0.17%, mid).

How common is RBP1 p.Arg9= (c.27C>G) in the general population?

RBP1 p.Arg9= (c.27C>G) is rare (popmax 0.17%, mid) (gnomAD).

RBP1 p.Arg9=

c.27C>G · rs754785993 · VCV1657363

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.17%, mid)

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -0.33	GERP -2.6
Overall
CADD	9.267	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.17% Middle Eastern · 9/5,292 alleles

Filtering AF 0.0886% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0663%

Overall 0.0103% 153/1,490,610 alleles · rare exomes 140/1,338,402 · genomes 13/152,208 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.17%	588
South Asian	0.0121%	8,280
European (non-Finnish)	0.0112%	8,926
Remaining individualsnot grpmax-eligible	0.0105%	9,556
African / African-American	0.00424%	23,596
Finnishnot grpmax-eligible	0.00177%	56,610

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: RBP1
Protein: p.Arg9=
Coding: c.27C>G
MANE Select: NM_002899
dbSNP: rs754785993
Type: single nucleotide variant
Location: chr3:139539692 (GRCh38)

Full RBP1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

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/rbp1-p-arg9 (accessed [today's date]).

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