Is ATP2B4 p.Pro613= (c.1839A>T) pathogenic?

ATP2B4 p.Pro613= (c.1839A>T) is classified Benign in ATP2B4 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-07-07). Rare (popmax 0.969%, afr).

How common is ATP2B4 p.Pro613= (c.1839A>T) in the general population?

ATP2B4 p.Pro613= (c.1839A>T) is rare (popmax 0.969%, afr) (gnomAD).

ATP2B4 p.Pro613=

c.1839A>T · rs61731212 · VCV704204

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

rare (popmax 0.969%, afr)

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 -4.2	GERP -2.7
Overall
CADD	1.564	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.969% African / African-American · 727/75,038 alleles

Filtering AF 0.91% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.887%

Overall 0.0512% 827/1,614,072 alleles · rare exomes 417/1,461,788 · genomes 410/152,284 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.969%	103
Middle Eastern	0.115%	866
Remaining individualsnot grpmax-eligible	0.0688%	1,454
Admixed American	0.0583%	1,715
European (non-Finnish)	0.00127%	78,666

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: ATP2B4
Protein: p.Pro613=
Coding: c.1839A>T
MANE Select: NM_001684
dbSNP: rs61731212
Type: single nucleotide variant
Location: chr1:203710916 (GRCh38)
Gene constraint: LOEUF 0.44 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 72.71 · 2 PDB

Full ATP2B4 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ATP2B4 p.Arg554Cys Uncertain significance ★★ same type
ATP2B4 p.Arg624Cys Uncertain significance ★★ same type
ATP2B4 p.Arg732Cys Uncertain significance ★★ same type
ATP2B4 p.Arg993Gly Uncertain significance ★★ same type
ATP2B4 p.Asn851Ser Uncertain significance ★★ same type
ATP2B4 p.Asp333Gly Uncertain significance ★★ same type
ATP2B4 p.Asp502Asn Uncertain significance ★★ same type
ATP2B4 p.Gly634Arg 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/atp2b4-p-pro613 (accessed [today's date]).

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