Is CBARP p.Arg535= (c.1605C>A) pathogenic?

CBARP p.Arg535= (c.1605C>A) is classified Likely benign in CBARP (ClinVar, Multiple submitters, 2 submitters; last evaluated 2023-01-13). Rare (popmax 0.52%, nfe).

How common is CBARP p.Arg535= (c.1605C>A) in the general population?

CBARP p.Arg535= (c.1605C>A) is rare (popmax 0.52%, nfe) (gnomAD).

CBARP p.Arg535=

c.1605C>A · rs763053321 · VCV2648908

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

rare (popmax 0.52%, 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 -1.4	GERP -2.2
Overall
CADD	0.894	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.52% European (non-Finnish) · 4,497/864,364 alleles

Filtering AF 0.508% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.502%

Overall 0.449% 4,724/1,053,050 alleles · rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.52%	192
Remaining individualsnot grpmax-eligible	0.422%	237
Admixed American	0.18%	556
African / African-American	0.0735%	1,361
South Asian	0.036%	2,778
Ashkenazi Jewishnot grpmax-eligible	0.00872%	11,474
Finnishnot grpmax-eligible	0.00743%	13,466

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: CBARP
Protein: p.Arg535=
Coding: c.1605C>A
MANE Select: NM_001393918
dbSNP: rs763053321
Type: single nucleotide variant
Location: chr19:1229692 (GRCh38)
Gene constraint: LOEUF 1.107 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 52.23
Residue 535: the 'disordered' region

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

Similar variants

CBARP c.1154+114C>G Uncertain significance ★ same type
CBARP c.1154+126G>T Uncertain significance ★ same type
CBARP c.1154+36C>G Uncertain significance ★ same type
CBARP c.1154+45C>T Uncertain significance ★ same type
CBARP c.1154+80G>A Uncertain significance ★ same type
CBARP c.1154+87C>T Uncertain significance ★ same type
CBARP p.Ala19Val Uncertain significance ★ ⚠ same type
CBARP p.Ala237= 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/cbarp-p-arg535 (accessed [today's date]).

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