Is DPF3 p.Val37Met (c.109G>A) pathogenic?

DPF3 p.Val37Met (c.109G>A) is classified Uncertain significance in DPF3 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-04-17). AlphaMissense: likely benign (0.3062); Ultra-rare (popmax 0.0594%, nfe).

How common is DPF3 p.Val37Met (c.109G>A) in the general population?

DPF3 p.Val37Met (c.109G>A) is ultra-rare (popmax 0.0594%, nfe) (gnomAD).

What do computational predictors say about DPF3 p.Val37Met (c.109G>A)?

AlphaMissense predicts likely benign (score 0.3062) — an in-silico prediction, not a clinical call.

DPF3 p.Val37Met

c.109G>A · rs199742673 · VCV3085451

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.3062 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0594%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.3062	likely benign
REVEL	0.236	benign-leaning
SaProt	LLR -8.28	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 1.5, phastCons 1
Regional constraint	o/e 0.91	unconstrained · MANE · 220 kb · p 0.076 · regional, not allelic
Overall
CADD	23.7	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

Grpmax group 0.0594% European (non-Finnish) · 701/1,179,838 alleles

Filtering AF 0.0558% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0542%

Overall 0.0453% 731/1,613,688 alleles · ultra-rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0594%	1,683
Remaining individualsnot grpmax-eligible	0.0208%	4,804
African / African-American	0.012%	8,321
East Asian	0.00669%	14,951
Admixed American	0.00667%	14,997
Finnishnot grpmax-eligible	0.00156%	64,014

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: DPF3
Protein: p.Val37Met
Coding: c.109G>A
MANE Select: NM_001280542
dbSNP: rs199742673
Type: single nucleotide variant
Location: chr14:72771817 (GRCh38)
Gene constraint: LOEUF 0.491 · pLI 0.99 (gnomAD)
Structure: AlphaFold pLDDT 73.58 · 8 PDB

Full DPF3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DPF3 c.871+2959C>T Uncertain significance ★★ same type
DPF3 p.Leu85= Benign ★★ same type
DPF3 c.871+2937G>T Uncertain significance ★ same type
DPF3 c.871+2946G>A Uncertain significance ★ same type
DPF3 c.871+2953G>A Uncertain significance ★ same type
DPF3 c.871+2958A>G Uncertain significance ★ same type
DPF3 c.871+3006C>T Uncertain significance ★ same type
DPF3 c.871+3020G>C 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/dpf3-p-val37met (accessed [today's date]).

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