Is DAB2IP p.Ala1003= (c.3009C>T) pathogenic?

DAB2IP p.Ala1003= (c.3009C>T) is classified Likely benign in DAB2IP (ClinVar, Single submitter, 1 submitter; last evaluated 2017-11-24). Ultra-rare (popmax 0.0164%, mid).

How common is DAB2IP p.Ala1003= (c.3009C>T) in the general population?

DAB2IP p.Ala1003= (c.3009C>T) is ultra-rare (popmax 0.0164%, mid) (gnomAD).

DAB2IP p.Ala1003=

c.3009C>T · rs141080470 · VCV728874

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0164%, mid)

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 -1.7	GERP -3.8
Overall
CADD	9.676	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0164% Middle Eastern · 1/6,080 alleles

Filtering AF 0.0035% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00318%

Overall 0.00397% 64/1,613,472 alleles · ultra-rare

Ancestry group	Frequency	1 in
Amishnot grpmax-eligible	0.329%	304
Middle Easterngrpmax	0.0164%	6,080
European (non-Finnish)	0.00449%	22,261
South Asian	0.0044%	22,749
Admixed American	0.00167%	59,964
Remaining individualsnot grpmax-eligible	0.0016%	62,462
African / African-American	0.00134%	74,872

Amish 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: DAB2IP
Protein: p.Ala1003=
Coding: c.3009C>T
MANE Select: NM_001395010
dbSNP: rs141080470
Type: single nucleotide variant
Location: chr9:121774301 (GRCh38)
Gene constraint: LOEUF 0.407 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 65.74

Full DAB2IP gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DAB2IP p.Ala816Thr Benign ★★ same type
DAB2IP p.Arg199= Benign ★★ same type
DAB2IP p.Arg966His Benign ★★ same type
DAB2IP p.Asp97= Benign/Likely benign ★★ same type
DAB2IP p.Lys284= Benign ★★ same type
DAB2IP p.Pro126= Likely benign ★★ same type
DAB2IP p.Ser460Leu Benign ★★ ⚠ same type
DAB2IP p.Ser68= Likely benign ★★ 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/dab2ip-p-ala1003 (accessed [today's date]).

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