Is DAZAP1 p.Arg88Trp (c.262C>T) pathogenic?

DAZAP1 p.Arg88Trp (c.262C>T) is classified Uncertain significance in DAZAP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-12-20). AlphaMissense: likely pathogenic (0.9952); Very rare (popmax 0.00223%, eas).

How common is DAZAP1 p.Arg88Trp (c.262C>T) in the general population?

DAZAP1 p.Arg88Trp (c.262C>T) is very rare (popmax 0.00223%, eas) (gnomAD).

What do computational predictors say about DAZAP1 p.Arg88Trp (c.262C>T)?

AlphaMissense predicts likely pathogenic (score 0.9952) — an in-silico prediction, not a clinical call.

DAZAP1 p.Arg88Trp

c.262C>T · rs773612058 · VCV3080133

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9952 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00223%, eas)

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.9952	likely pathogenic
REVEL	0.818	moderately pathogenic-leaning
SaProt	LLR -13.98	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.6	GERP 1.6, phastCons 1
Regional constraint	o/e 0.63	unconstrained · MANE · 13 kb · p 4.2e-06 · regional, not allelic
Overall
CADD	34.0	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — 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 0.00223% East Asian · 1/44,872 alleles

Overall 0.000137% 2/1,461,628 alleles · very rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00223%	44,872
European (non-Finnish)	8.48e-05%	1,179,874

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: DAZAP1
Protein: p.Arg88Trp
Coding: c.262C>T
MANE Select: NM_018959
dbSNP: rs773612058
Type: single nucleotide variant
Location: chr19:1418690 (GRCh38)
Gene constraint: LOEUF 0.236 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 65.53 · 2 PDB
Residue 88: the rrm 1 domain; the 'disordered' region

Full DAZAP1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DAZAP1 p.Pro271= Benign ★★ same type
DAZAP1 p.Ala214Thr Uncertain significance ★ ⚠ same type
DAZAP1 p.Ala242Thr Uncertain significance ★ ⚠ same type
DAZAP1 p.Ala251Gly Uncertain significance ★ ⚠ same type
DAZAP1 p.Ala255Val Uncertain significance ★ ⚠ same type
DAZAP1 p.Ala331Val Uncertain significance ★ ⚠ same type
DAZAP1 p.Ala340Thr Uncertain significance ★ ⚠ same type
DAZAP1 p.Arg96Trp 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/dazap1-p-arg88trp (accessed [today's date]).

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