Is ABCA7 p.Ile853= (c.2559C>T) pathogenic?

ABCA7 p.Ile853= (c.2559C>T) is classified Likely benign in ABCA7 (ClinVar, Single submitter, 1 submitter; last evaluated 2018-12-17). Very rare (popmax 0.00223%, eas).

How common is ABCA7 p.Ile853= (c.2559C>T) in the general population?

ABCA7 p.Ile853= (c.2559C>T) is very rare (popmax 0.00223%, eas) (gnomAD).

ABCA7 p.Ile853=

c.2559C>T · rs1599639271 · VCV798866

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00223%, eas)

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 0.77	GERP 1.9, phastCons 0.99
Overall
CADD	5.241	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00223% East Asian · 1/44,760 alleles

Overall 0.000138% 2/1,452,934 alleles · very rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00223%	44,760
Remaining individualsnot grpmax-eligible	0.00161%	62,144

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: ABCA7
Protein: p.Ile853=
Coding: c.2559C>T
MANE Select: NM_019112
dbSNP: rs1599639271
Type: single nucleotide variant
Location: chr19:1050927 (GRCh38)
Gene constraint: LOEUF 1.368 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 75.77 · 6 PDB
Residue 853: an α-helix; the abc transporter 1 domain

Full ABCA7 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ABCA7 c.2684+5G>A Uncertain significance ★★ same type
ABCA7 c.3578-2A>G Uncertain significance ★★ same type
ABCA7 p.Arg1026Cys Uncertain significance ★★ ⚠ same type
ABCA7 p.Arg652Cys Uncertain significance ★★ ⚠ same type
ABCA7 p.Arg880Trp Uncertain significance ★★ ⚠ same type
ABCA7 p.Asp1452Asn Uncertain significance ★★ ⚠ same type
ABCA7 p.Asp2085Asn Uncertain significance ★★ ⚠ same type
ABCA7 p.Gln925Ter 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/abca7-p-ile853 (accessed [today's date]).

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