Is ATP9B p.Phe570= (c.1710C>T) pathogenic?

ATP9B p.Phe570= (c.1710C>T) is classified Benign in ATP9B (ClinVar, Multiple submitters, 2 submitters; last evaluated 2018-04-20). Common (popmax 7.94%, afr) — too common for a highly-penetrant pathogenic allele.

ATP9B p.Phe570=

Q: How common is ATP9B p.Phe570= (c.1710C>T) in the general population?

ATP9B p.Phe570= (c.1710C>T) is common (popmax 7.94%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.1710C>T · rs34339254 · VCV790747

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Common

common (popmax 7.94%, afr) — too common for a highly-penetrant pathogenic allele

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 -4.4	GERP -3.3
Overall
CADD	0.604	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 7.94% African / African-American · 5,959/75,034 alleles

Filtering AF 7.77% ClinGen BA1/BS1 input FAF95, joint · FAF99 7.7%

Overall 0.431% 6,959/1,614,182 alleles · common

Ancestry group	Frequency	1 in
African / African-Americangrpmax	7.94%	13
Admixed American	0.595%	168
Remaining individualsnot grpmax-eligible	0.554%	181
Middle Eastern	0.28%	357
European (non-Finnish)	0.0222%	4,504
South Asian	0.0187%	5,357
Ashkenazi Jewishnot grpmax-eligible	0.00338%	29,606

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: ATP9B
Protein: p.Phe570=
Coding: c.1710C>T
MANE Select: NM_198531
dbSNP: rs34339254
Type: single nucleotide variant
Location: chr18:79307171 (GRCh38)
Gene constraint: LOEUF 0.857 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 79.49

Full ATP9B gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ATP9B p.Thr353Ala Uncertain significance ★★ ⚠ same type
ATP9B p.Asp504Asn Benign ★★ same type
ATP9B p.Leu384= Benign ★★ same type
ATP9B p.Thr117= Benign ★★ same type
ATP9B p.Ala1044Val Uncertain significance ★ ⚠ same type
ATP9B p.Ala1049Thr Uncertain significance ★ ⚠ same type
ATP9B p.Ala1085Pro Uncertain significance ★ ⚠ same type
ATP9B p.Ala1085Thr 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/atp9b-p-phe570 (accessed [today's date]).

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