Is DPF1 p.Ser10= (c.30C>T) pathogenic?

DPF1 p.Ser10= (c.30C>T) is classified Likely benign in DPF1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-02-26). Very rare (popmax 0.00386%, nfe).

How common is DPF1 p.Ser10= (c.30C>T) in the general population?

DPF1 p.Ser10= (c.30C>T) is very rare (popmax 0.00386%, nfe) (gnomAD).

DPF1 p.Ser10=

c.30C>T · VCV3842203

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00386%, nfe)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.101	moderately benign-leaning
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · G>C here scores Δ0.21 · evaluated, not missing
Constraint at this position
Conservation	phyloP 7.4	GERP 0.71, phastCons 1
Overall
CADD	18.23	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00386% European (non-Finnish) · 45/1,165,800 alleles

Filtering AF 0.00294% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00263%

Overall 0.00296% 47/1,586,568 alleles · very rare exomes 42/1,434,342 · genomes 5/152,226 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00386%	25,907
East Asian	0.00232%	43,072
African / African-American	0.00137%	73,006

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: DPF1
Protein: p.Ser10=
Coding: c.30C>T
MANE Select: NM_001135155
Type: single nucleotide variant
Location: chr19:38222708 (GRCh38)
Gene constraint: LOEUF 0.415 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 67.41

Full DPF1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DPF1 c.778+2T>G Uncertain significance ★ same type
DPF1 c.-17A>C Uncertain significance ★ same type
DPF1 c.-35C>A Uncertain significance ★ same type
DPF1 p.Ala186Pro Uncertain significance ★ ⚠ same type
DPF1 p.Ala32Thr Uncertain significance ★ same type
DPF1 p.Ala380Ser Uncertain significance ★ same type
DPF1 p.Ala66Asp Uncertain significance ★ same type
DPF1 p.Arg230His 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/dpf1-p-ser10 (accessed [today's date]).

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