Is DAZAP2 p.Asn146= (c.438C>T) pathogenic?

DAZAP2 p.Asn146= (c.438C>T) is classified Likely benign in DAZAP2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-05-09). Ultra-rare (popmax 0.036%, afr).

How common is DAZAP2 p.Asn146= (c.438C>T) in the general population?

DAZAP2 p.Asn146= (c.438C>T) is ultra-rare (popmax 0.036%, afr) (gnomAD).

DAZAP2 p.Asn146=

c.438C>T · VCV4009441

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.036%, afr)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.151	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.099	GERP -4.9, phastCons 0.71
Overall
CADD	8.076	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.036% African / African-American · 27/75,042 alleles

Filtering AF 0.0254% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0218%

Overall 0.00229% 37/1,613,858 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.036%	2,779
South Asian	0.0033%	30,345
Remaining individualsnot grpmax-eligible	0.0016%	62,500
European (non-Finnish)	0.000509%	196,643

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.Asn146=
Coding: c.438C>T
MANE Select: NM_014764
Type: single nucleotide variant
Location: chr12:51242389 (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.Asn146Thr Uncertain significance ★ ⚠ same residue
DAZAP2 p.Asn146Ser Likely benign ★ ⚠ 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

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-asn146 (accessed [today's date]).

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