Is BDP1 p.Arg2530= (c.7590C>T) pathogenic?

BDP1 p.Arg2530= (c.7590C>T) is classified Benign in BDP1 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2017-05-09). Common (popmax 56.6%, amr) — too common for a highly-penetrant pathogenic allele.

BDP1 p.Arg2530=

Q: How common is BDP1 p.Arg2530= (c.7590C>T) in the general population?

BDP1 p.Arg2530= (c.7590C>T) is common (popmax 56.6%, amr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.7590C>T · rs277941 · VCV517820

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Common

common (popmax 56.6%, amr) — too common for a highly-penetrant pathogenic allele

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 -0.031	GERP 3, phastCons 0.001
Overall
CADD	1.583	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 56.6% Admixed American · 33,916/59,920 alleles

Filtering AF 56.1% ClinGen BA1/BS1 input FAF95, joint · FAF99 55.9%

Overall 34.1% 548,882/1,611,860 alleles · common

Ancestry group	Frequency	1 in
Admixed Americangrpmax	56.6%	2
East Asian	50.2%	2
Ashkenazi Jewishnot grpmax-eligible	41.1%	2
Middle Eastern	35.2%	3
Remaining individualsnot grpmax-eligible	34.2%	3
European (non-Finnish)	34.1%	3
Finnishnot grpmax-eligible	29%	3
South Asian	27.6%	4
Amishnot grpmax-eligible	17.6%	6
African / African-American	14.2%	7

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: BDP1
Protein: p.Arg2530=
Coding: c.7590C>T
MANE Select: NM_018429
dbSNP: rs277941
Type: single nucleotide variant
Location: chr5:71562367 (GRCh38)
Gene constraint: LOEUF 0.683 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 37.23 · 13 PDB
Residue 2530: the 'disordered' region

Full BDP1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

BDP1 p.Arg2530Cys Uncertain significance ★ ⚠ same residue
BDP1 p.Arg880Gly Uncertain significance ★★ ⚠ same type
BDP1 p.Arg935Ile Uncertain significance ★★ ⚠ same type
BDP1 p.Asp1875Asn Uncertain significance ★★ ⚠ same type
BDP1 p.Glu1139Val Uncertain significance ★★ ⚠ same type
BDP1 p.Ile1035Met Uncertain significance ★★ ⚠ same type
BDP1 p.Lys1304Glu Uncertain significance ★★ ⚠ same type
BDP1 p.Lys354Glu 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/bdp1-p-arg2530 (accessed [today's date]).

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