Is DPF2 p.Gln288His (c.864A>C) pathogenic?

DPF2 p.Gln288His (c.864A>C) is classified Uncertain significance in DPF2 (ClinVar, Single submitter, 1 submitter; last evaluated 2018-08-23). AlphaMissense: likely benign (0.1492); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with DPF2 p.Gln288His (c.864A>C)?

DPF2 p.Gln288His (c.864A>C) is associated with Inborn genetic diseases (ClinVar).

How common is DPF2 p.Gln288His (c.864A>C) in the general population?

DPF2 p.Gln288His (c.864A>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about DPF2 p.Gln288His (c.864A>C)?

AlphaMissense predicts likely benign (score 0.1492) — an in-silico prediction, not a clinical call.

DPF2 p.Gln288His

c.864A>C · rs373762591 · VCV985635

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1492 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.1492	likely benign
REVEL	0.579	indeterminate
SaProt	LLR -8.10	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.42	GERP -3.7, phastCons 0.001
Regional constraint	o/e 0.69	unconstrained · MANE · 341 bp · p 0.0039 · regional, not allelic
Overall
CADD	8.121	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: DPF2
Protein: p.Gln288His
Coding: c.864A>C
MANE Select: NM_006268
dbSNP: rs373762591
Type: single nucleotide variant
Location: chr11:65346018 (GRCh38)
Gene constraint: LOEUF 0.287 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 69.62 · 9 PDB

Full DPF2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

DPF2 c.904+1G>A Pathogenic ★★ same condition
DPF2 p.Ala133Pro Uncertain significance ★★ ⚠ same condition
DPF2 p.Arg77Gln Uncertain significance ★★ ⚠ same condition
DPF2 p.Arg83Trp Uncertain significance ★★ ⚠ same condition
DPF2 p.Asn26Ser Uncertain significance ★★ ⚠ same condition
DPF2 p.Asp141Gly Uncertain significance ★★ ⚠ same condition
DPF2 p.Glu173Gly Uncertain significance ★★ ⚠ same condition
DPF2 p.Gly189Val Uncertain significance ★★ ⚠ same condition

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/dpf2-p-gln288his (accessed [today's date]).

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