Is DAZAP2 p.Val149Ile (c.445G>A) pathogenic?

DAZAP2 p.Val149Ile (c.445G>A) is classified Uncertain significance in DAZAP2 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-11-20). AlphaMissense: likely benign (0.1663); Ultra-rare (popmax 0.0233%, amr).

How common is DAZAP2 p.Val149Ile (c.445G>A) in the general population?

DAZAP2 p.Val149Ile (c.445G>A) is ultra-rare (popmax 0.0233%, amr) (gnomAD).

What do computational predictors say about DAZAP2 p.Val149Ile (c.445G>A)?

AlphaMissense predicts likely benign (score 0.1663) — an in-silico prediction, not a clinical call.

DAZAP2 p.Val149Ile

c.445G>A · VCV3499732

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1663 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0233%, amr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1663	likely benign
REVEL	0.11	moderately benign-leaning
SaProt	LLR -7.23	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
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 0.80	unconstrained · MANE · 3,547 bp · p 0.0028 · regional, not allelic
Overall
CADD	22.2	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0233% Admixed American · 14/60,014 alleles

Filtering AF 0.0141% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0112%

Overall 0.00142% 23/1,614,076 alleles · ultra-rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0233%	4,287
African / African-American	0.00267%	37,513
Remaining individualsnot grpmax-eligible	0.0016%	62,510
European (non-Finnish)	0.000508%	196,663

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: DAZAP2
Protein: p.Val149Ile
Coding: c.445G>A
MANE Select: NM_014764
Type: single nucleotide variant
Location: chr12:51242396 (GRCh38)
Gene constraint: LOEUF 0.457 · pLI 0.98 (gnomAD)
Structure: AlphaFold pLDDT 58.37

Full DAZAP2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DAZAP2 p.Val149Leu Uncertain significance ★ ⚠ same residue
DAZAP2 c.*118G>A Uncertain significance ★ same type
DAZAP2 c.*24G>A Uncertain significance ★ same type
DAZAP2 c.*50C>G Uncertain significance ★ same type
DAZAP2 c.*51T>G Uncertain significance ★ same type
DAZAP2 c.*58A>G Uncertain significance ★ same type
DAZAP2 c.*5C>G Uncertain significance ★ same type
DAZAP2 p.Ala79Thr 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/dazap2-p-val149ile (accessed [today's date]).

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