Is DAZAP1 p.Pro370Thr (c.1108C>A) pathogenic?

DAZAP1 p.Pro370Thr (c.1108C>A) is classified Uncertain significance in DAZAP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-01-31). AlphaMissense: likely benign (0.0597); Absent from gnomAD v4.1.

How common is DAZAP1 p.Pro370Thr (c.1108C>A) in the general population?

DAZAP1 p.Pro370Thr (c.1108C>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about DAZAP1 p.Pro370Thr (c.1108C>A)?

AlphaMissense predicts likely benign (score 0.0597) — an in-silico prediction, not a clinical call.

DAZAP1 p.Pro370Thr

c.1108C>A · VCV3838300

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0597 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0597	likely benign
REVEL	0.095	moderately benign-leaning
SaProt	LLR -8.47	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 1.4, phastCons 1
Regional constraint	o/e 0.78	unconstrained · MANE · 6,046 bp · p 9e-05 · regional, not allelic
Overall
CADD	21.1	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

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: DAZAP1
Protein: p.Pro370Thr
Coding: c.1108C>A
MANE Select: NM_018959
Type: single nucleotide variant
Location: chr19:1434796 (GRCh38)
Gene constraint: LOEUF 0.236 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 65.53 · 2 PDB
Residue 370: 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.Arg88Trp 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-pro370thr (accessed [today's date]).

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