Is DPF2 p.Arg83Gln (c.248G>A) pathogenic?

DPF2 p.Arg83Gln (c.248G>A) is classified Likely benign in DPF2 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-11-12). AlphaMissense: likely pathogenic (0.6412); Ultra-rare (popmax 0.03%, amr); Associated with Inborn genetic diseases.

What condition is associated with DPF2 p.Arg83Gln (c.248G>A)?

DPF2 p.Arg83Gln (c.248G>A) is associated with Inborn genetic diseases (ClinVar).

How common is DPF2 p.Arg83Gln (c.248G>A) in the general population?

DPF2 p.Arg83Gln (c.248G>A) is ultra-rare (popmax 0.03%, amr) (gnomAD).

What do computational predictors say about DPF2 p.Arg83Gln (c.248G>A)?

AlphaMissense predicts likely pathogenic (score 0.6412) — an in-silico prediction, not a clinical call.

DPF2 p.Arg83Gln

c.248G>A · rs199801105 · VCV1603274

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely pathogenic

0.6412 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.03%, amr)

Missense predictors

2/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.6412	likely pathogenic
REVEL	0.685	pathogenic-leaning
SaProt	LLR -6.20	tolerated
⇒ AlphaMissense and REVEL call this damaging; SaProt does not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 1.7, phastCons 1
Regional constraint	o/e 0.83	unconstrained · MANE · 10 kb · p 0.0043 · regional, not allelic
Overall
CADD	32.0	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.03% Admixed American · 18/60,016 alleles

Filtering AF 0.0194% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.016%

Overall 0.00217% 35/1,614,114 alleles · ultra-rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.03%	3,334
Middle Eastern	0.0165%	6,060
East Asian	0.00446%	22,443
African / African-American	0.00133%	75,040
European (non-Finnish)	0.0011%	90,772

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: DPF2
Protein: p.Arg83Gln
Coding: c.248G>A
MANE Select: NM_006268
dbSNP: rs199801105
Type: single nucleotide variant
Location: chr11:65341020 (GRCh38)
Gene constraint: LOEUF 0.287 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 69.62 · 9 PDB
Residue 83: the 'disordered' region

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 p.Arg83Trp Uncertain significance ★★ ⚠ same residue
DPF2 p.Arg83Pro Uncertain significance ★ ⚠ same residue
DPF2 p.Arg83= Likely benign ★ same residue
DPF2 c.904+1G>A Pathogenic ★★ same condition
DPF2 p.Ala133Pro Uncertain significance ★★ ⚠ same condition
DPF2 p.Arg77Gln Uncertain significance ★★ ⚠ same condition
DPF2 p.Asn26Ser Uncertain significance ★★ ⚠ same condition
DPF2 p.Asp141Gly 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-arg83gln (accessed [today's date]).

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