Is DAB2IP p.Met894Lys (c.2681T>A) pathogenic?

DAB2IP p.Met894Lys (c.2681T>A) is classified Uncertain significance in DAB2IP (ClinVar, Single submitter, 1 submitter; last evaluated 2024-11-19). AlphaMissense: ambiguous (0.381); Very rare (popmax 0.00345%, nfe).

How common is DAB2IP p.Met894Lys (c.2681T>A) in the general population?

DAB2IP p.Met894Lys (c.2681T>A) is very rare (popmax 0.00345%, nfe) (gnomAD).

What do computational predictors say about DAB2IP p.Met894Lys (c.2681T>A)?

AlphaMissense predicts ambiguous (score 0.381) — an in-silico prediction, not a clinical call.

DAB2IP p.Met894Lys

c.2681T>A · VCV3499534

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.381 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00345%, nfe)

Missense predictors

0/2 damaging

REVEL, SaProt · AlphaMissense no call

Computational evidence

Protein change
AlphaMissense	0.381	ambiguous
REVEL	0.049	moderately benign-leaning
SaProt	LLR -6.23	tolerated
⇒ REVEL and SaProt both call this tolerated; AlphaMissense makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 5.9	GERP 2.4, phastCons 1
Regional constraint	o/e 0.91	unconstrained · MANE · 9,835 bp · p 0.021 · regional, not allelic
Overall
CADD	22.5	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00345% European (non-Finnish) · 40/1,159,478 alleles

Filtering AF 0.0026% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00229%

Overall 0.00261% 41/1,570,906 alleles · very rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00345%	28,987
African / African-American	0.00135%	73,880

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.Met894Lys
Coding: c.2681T>A
MANE Select: NM_001395010
Type: single nucleotide variant
Location: chr9:121773209 (GRCh38)
Gene constraint: LOEUF 0.407 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 65.74
Residue 894: the 'necessary for interaction with akt1' region

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-met894lys (accessed [today's date]).

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