Is ABCA7 p.Leu1297= (c.3891C>T) pathogenic?

ABCA7 p.Leu1297= (c.3891C>T) is classified Likely benign in ABCA7 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-08-05). Very rare (popmax 0.00234%, eas); Associated with ABCA7-related disorder.

What condition is associated with ABCA7 p.Leu1297= (c.3891C>T)?

ABCA7 p.Leu1297= (c.3891C>T) is associated with ABCA7-related disorder (ClinVar).

How common is ABCA7 p.Leu1297= (c.3891C>T) in the general population?

ABCA7 p.Leu1297= (c.3891C>T) is very rare (popmax 0.00234%, eas) (gnomAD).

ABCA7 p.Leu1297=

c.3891C>T · rs368024653 · VCV3035412

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00234%, eas)

Conditions

ABCA7-related disorder

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 -9.4	GERP -2.4
Overall
CADD	0.057	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00234% East Asian · 1/42,658 alleles

Filtering AF 0.00055% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000435%

Overall 0.000887% 14/1,577,944 alleles · very rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00234%	42,658
Remaining individualsnot grpmax-eligible	0.00164%	61,094
European (non-Finnish)	0.00103%	96,888

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.Leu1297=
Coding: c.3891C>T
MANE Select: NM_019112
dbSNP: rs368024653
Type: single nucleotide variant
Location: chr19:1054819 (GRCh38)
Gene constraint: LOEUF 1.368 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 75.77 · 6 PDB
Residue 1297: an α-helix

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

Disease context

ABCA7-related disorder

Similar variants

ABCA7 c.4417-1G>C Likely pathogenic ★ same condition
ABCA7 p.Gln1083Ter Pathogenic ★ same condition
ABCA7 p.Arg1754Ter Likely pathogenic same condition
ABCA7 p.Glu269Ter Likely pathogenic same condition
ABCA7 c.790+10T>G Benign same condition
ABCA7 c.-9A>G Benign same condition
ABCA7 p.Ala1441= Likely benign same condition
ABCA7 p.Ala1864= Benign same condition

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-leu1297 (accessed [today's date]).

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