Is ATP2B2 p.Pro945= (c.2835G>A) pathogenic?

ATP2B2 p.Pro945= (c.2835G>A) is classified Likely benign in ATP2B2 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2024-11-01). Ultra-rare (popmax 0.0108%, nfe).

How common is ATP2B2 p.Pro945= (c.2835G>A) in the general population?

ATP2B2 p.Pro945= (c.2835G>A) is ultra-rare (popmax 0.0108%, nfe) (gnomAD).

ATP2B2 p.Pro945=

c.2835G>A · rs374714860 · VCV745074

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0108%, 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 -2.8	GERP -4.1
Overall
CADD	9.359	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0108% European (non-Finnish) · 128/1,179,928 alleles

Filtering AF 0.00928% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00871%

Overall 0.00898% 145/1,613,822 alleles · ultra-rare

Ancestry group	Frequency	1 in
Finnishnot grpmax-eligible	0.0156%	6,402
European (non-Finnish)grpmax	0.0108%	9,218
Remaining individualsnot grpmax-eligible	0.0064%	15,622
East Asian	0.00223%	44,862
Admixed American	0.00167%	59,992
South Asian	0.0011%	91,072

Finnish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: ATP2B2
Protein: p.Pro945=
Coding: c.2835G>A
MANE Select: NM_001001331
dbSNP: rs374714860
Type: single nucleotide variant
Location: chr3:10342834 (GRCh38)
Gene constraint: LOEUF 0.19 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 73.83
Residue 945: a UniProt-annotated variant site (in dfna82)

Full ATP2B2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ATP2B2 p.Pro945Leu Uncertain significance ★ ⚠ same residue
ATP2B2 c.2136+1G>A Pathogenic/Likely pathogenic ★★ same type
ATP2B2 p.Arg1132Ter Pathogenic/Likely pathogenic ★★ same type
ATP2B2 p.Glu457Lys Likely pathogenic ★★ same type
ATP2B2 p.Gly821Arg Pathogenic ★★ same type
ATP2B2 p.Thr503Met Pathogenic/Likely pathogenic ★★ same type
ATP2B2 c.2316+5G>A Uncertain significance ★★ same type
ATP2B2 c.3420+1998G>T 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/atp2b2-p-pro945 (accessed [today's date]).

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