Is BDP1 p.Ser1526= (c.4578A>G) pathogenic?

BDP1 p.Ser1526= (c.4578A>G) is classified Benign/Likely benign in BDP1 (ClinVar, Multiple submitters, 4 submitters; last evaluated 2024-11-11). Rare (popmax 0.277%, nfe).

How common is BDP1 p.Ser1526= (c.4578A>G) in the general population?

BDP1 p.Ser1526= (c.4578A>G) is rare (popmax 0.277%, nfe) (gnomAD).

BDP1 p.Ser1526=

c.4578A>G · rs199669834 · VCV508594

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

rare (popmax 0.277%, 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 -0.023	GERP -4
Overall
CADD	1.503	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.277% European (non-Finnish) · 3,273/1,179,620 alleles

Filtering AF 0.27% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.266%

Overall 0.219% 3,536/1,613,182 alleles · rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.277%	360
Ashkenazi Jewishnot grpmax-eligible	0.189%	528
Remaining individualsnot grpmax-eligible	0.187%	534
African / African-American	0.0534%	1,873
Finnishnot grpmax-eligible	0.0422%	2,371
Admixed American	0.0384%	2,604

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.Ser1526=
Coding: c.4578A>G
MANE Select: NM_018429
dbSNP: rs199669834
Type: single nucleotide variant
Location: chr5:71515051 (GRCh38)
Gene constraint: LOEUF 0.683 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 37.23 · 13 PDB
Residue 1526: the 'disordered' region

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-ser1526 (accessed [today's date]).

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