ABCA2 p.Asp679=

Q: Is ABCA2 p.Asp679= (c.2037T>C) pathogenic?

ABCA2 p.Asp679= (c.2037T>C) is classified Benign/Likely benign in ABCA2 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2024-11-27). Common (popmax 99.8%, eas) — too common for a highly-penetrant pathogenic allele; Associated with intellectual developmental disorder with poor growth and with or without seizures or ataxia.

Q: What condition is associated with ABCA2 p.Asp679= (c.2037T>C)?

ABCA2 p.Asp679= (c.2037T>C) is associated with intellectual developmental disorder with poor growth and with or without seizures or ataxia (ClinVar).

Q: How common is ABCA2 p.Asp679= (c.2037T>C) in the general population?

ABCA2 p.Asp679= (c.2037T>C) is common (popmax 99.8%, eas) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.2037T>C · rs908832 · VCV1185362

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Common

common (popmax 99.8%, eas) — too common for a highly-penetrant pathogenic allele

Conditions

intellectual developmental disorder with poor growth and with or without seizures or ataxia

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 -1.2	GERP -2.3
Overall
CADD	3.061	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 99.8% East Asian · 44,763/44,872 alleles

Filtering AF 99% ClinGen BA1/BS1 input FAF95, joint · FAF99 98.7%

Overall 97.1% 1,566,338/1,612,726 alleles · common

Ancestry group	Frequency	1 in
East Asiangrpmax	99.8%	1
Admixed American	98.7%	1
Amishnot grpmax-eligible	98.6%	1
South Asian	97.7%	1
Middle Eastern	97.4%	1
Ashkenazi Jewishnot grpmax-eligible	97.3%	1
European (non-Finnish)	97.1%	1
Finnishnot grpmax-eligible	97%	1
Remaining individualsnot grpmax-eligible	97%	1
African / African-American	94%	1

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: ABCA2
Protein: p.Asp679=
Coding: c.2037T>C
MANE Select: NM_001606
dbSNP: rs908832
Type: single nucleotide variant
Location: chr9:137018032 (GRCh38)
Gene constraint: LOEUF 0.436 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 71.46
Residue 679: a UniProt-annotated variant site (in idpogsa)

Full ABCA2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

intellectual developmental disorder with poor growth and with or without seizures or ataxia — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

ABCA2 p.Gln1370Ter Likely pathogenic ★★ same condition
ABCA2 p.Ala367Thr Uncertain significance ★★ ⚠ same condition
ABCA2 p.Arg114Gln Uncertain significance ★★ ⚠ same condition
ABCA2 p.Arg1160His Uncertain significance ★★ ⚠ same condition
ABCA2 p.Arg1383His Uncertain significance ★★ ⚠ same condition
ABCA2 p.Arg1664Trp Uncertain significance ★★ ⚠ same condition
ABCA2 p.Arg954His Uncertain significance ★★ ⚠ same condition
ABCA2 p.Asn1755Lys Uncertain significance ★★ ⚠ 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/abca2-p-asp679 (accessed [today's date]).

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