Is DAXX p.Asp439= (c.1317C>T) pathogenic?

DAXX p.Asp439= (c.1317C>T) is classified Benign in DAXX (ClinVar, Single submitter, 1 submitter; last evaluated 2018-07-18). Rare (popmax 0.666%, afr).

How common is DAXX p.Asp439= (c.1317C>T) in the general population?

DAXX p.Asp439= (c.1317C>T) is rare (popmax 0.666%, afr) (gnomAD).

DAXX p.Asp439=

c.1317C>T · rs148860789 · VCV711441

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.666%, afr)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -4.9	GERP -2.5
Overall
CADD	3.424	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.666% African / African-American · 497/74,620 alleles

Filtering AF 0.618% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.598%

Overall 0.0488% 787/1,613,024 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.666%	150
Remaining individualsnot grpmax-eligible	0.0384%	2,604
Admixed American	0.0334%	2,995
European (non-Finnish)	0.0209%	4,796

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: DAXX
Protein: p.Asp439=
Coding: c.1317C>T
MANE Select: NM_001141969
dbSNP: rs148860789
Type: single nucleotide variant
Location: chr6:33320159 (GRCh38)
Gene constraint: LOEUF 0.524 · pLI 0.89 (gnomAD)
Structure: AlphaFold pLDDT 64.16 · 14 PDB
Residue 439: the 'necessary for interaction with usp7' region; the 'disordered' region

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

Similar variants

DAXX c.-56T>C Uncertain significance ★ same type
DAXX c.-63C>T Uncertain significance ★ same type
DAXX c.-66A>G Uncertain significance ★ same type
DAXX p.Ala103Val Uncertain significance ★ ⚠ same type
DAXX p.Ala396Val Uncertain significance ★ ⚠ same type
DAXX p.Ala545Gly Uncertain significance ★ ⚠ same type
DAXX p.Ala79Val Uncertain significance ★ ⚠ same type
DAXX p.Arg115Gln 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/daxx-p-asp439 (accessed [today's date]).

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