Is BDP1 p.Arg360Cys (c.1078C>T) pathogenic?

BDP1 p.Arg360Cys (c.1078C>T) is classified Likely benign in BDP1 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-11-13). AlphaMissense: likely pathogenic (0.8396); Rare (popmax 0.119%, nfe).

How common is BDP1 p.Arg360Cys (c.1078C>T) in the general population?

BDP1 p.Arg360Cys (c.1078C>T) is rare (popmax 0.119%, nfe) (gnomAD).

What do computational predictors say about BDP1 p.Arg360Cys (c.1078C>T)?

AlphaMissense predicts likely pathogenic (score 0.8396) — an in-silico prediction, not a clinical call.

BDP1 p.Arg360Cys

c.1078C>T · rs200036481 · VCV1318260

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely pathogenic

0.8396 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.119%, nfe)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.8396	likely pathogenic · top 5% in BDP1
REVEL	0.219	benign-leaning
SaProt	LLR -9.10	tolerated
⇒ AlphaMissense calls this damaging; REVEL and SaProt do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.7	GERP 1.6, phastCons 1
Regional constraint	o/e 0.99	unconstrained · MANE · 86 kb · p 0.66 · regional, not allelic
Overall
CADD	33.0	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 0.119% European (non-Finnish) · 1,378/1,155,614 alleles

Filtering AF 0.114% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.112%

Overall 0.096% 1,476/1,537,218 alleles · rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.119%	839
Remaining individualsnot grpmax-eligible	0.0878%	1,139
Middle Eastern	0.0876%	1,142
Admixed American	0.0385%	2,597
African / African-American	0.0159%	6,307
Finnishnot grpmax-eligible	0.011%	9,065
South Asian	0.00907%	11,025
Ashkenazi Jewishnot grpmax-eligible	0.00368%	27,200

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.Arg360Cys
Coding: c.1078C>T
MANE Select: NM_018429
dbSNP: rs200036481
Type: single nucleotide variant
Location: chr5:71486492 (GRCh38)
Gene constraint: LOEUF 0.683 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 37.23 · 13 PDB
Residue 360: the 'required for phosphorylation by csnk2a1' region

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

Similar variants

BDP1 p.Arg360His 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-arg360cys (accessed [today's date]).

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