Is BDP1 p.Arg504Ser (c.1512G>T) pathogenic?

BDP1 p.Arg504Ser (c.1512G>T) is classified Benign in BDP1 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2019-05-06). AlphaMissense: likely benign (0.2455); Low-frequency (popmax 2.57%, afr).

How common is BDP1 p.Arg504Ser (c.1512G>T) in the general population?

BDP1 p.Arg504Ser (c.1512G>T) is low-frequency (popmax 2.57%, afr) (gnomAD).

What do computational predictors say about BDP1 p.Arg504Ser (c.1512G>T)?

AlphaMissense predicts likely benign (score 0.2455) — an in-silico prediction, not a clinical call.

BDP1 p.Arg504Ser

c.1512G>T · rs7709578 · VCV515793

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.2455 · ACMG-weighted

gnomAD v4.1

Rare

low-frequency (popmax 2.57%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.2455	likely benign
REVEL	0.043	moderately benign-leaning
SaProt	LLR -4.37	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.004	GERP -2.5, phastCons 0.012
Regional constraint	o/e 0.99	unconstrained · MANE · 86 kb · p 0.66 · regional, not allelic
Overall
CADD	3.947	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 2.57% African / African-American · 1,924/74,950 alleles

Filtering AF 2.47% ClinGen BA1/BS1 input FAF95, joint · FAF99 2.43%

Overall 0.155% 2,494/1,611,082 alleles · low-frequency

Ancestry group	Frequency	1 in
African / African-Americangrpmax	2.57%	39
Middle Eastern	0.33%	303
Remaining individualsnot grpmax-eligible	0.277%	361
Admixed American	0.24%	417
European (non-Finnish)	0.0187%	5,333
South Asian	0.0122%	8,200
Finnishnot grpmax-eligible	0.00312%	32,002

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.Arg504Ser
Coding: c.1512G>T
MANE Select: NM_018429
dbSNP: rs7709578
Type: single nucleotide variant
Location: chr5:71491003 (GRCh38)
Gene constraint: LOEUF 0.683 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 37.23 · 13 PDB

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

Similar variants

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
BDP1 p.Pro1432Leu 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-arg504ser (accessed [today's date]).

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