Is DBF4 p.Lys579Glu (c.1735A>G) pathogenic?

DBF4 p.Lys579Glu (c.1735A>G) is classified Benign in DBF4 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2018-01-12). AlphaMissense: likely benign (0.3292); Low-frequency (popmax 1.41%, nfe).

How common is DBF4 p.Lys579Glu (c.1735A>G) in the general population?

DBF4 p.Lys579Glu (c.1735A>G) is low-frequency (popmax 1.41%, nfe) (gnomAD).

What do computational predictors say about DBF4 p.Lys579Glu (c.1735A>G)?

AlphaMissense predicts likely benign (score 0.3292) — an in-silico prediction, not a clinical call.

DBF4 p.Lys579Glu

c.1735A>G · rs61747462 · VCV779253

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.3292 · ACMG-weighted

gnomAD v4.1

Rare

low-frequency (popmax 1.41%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.3292	likely benign
REVEL	0.059	moderately benign-leaning
SaProt	LLR -7.44	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 7.8	GERP 2.4, phastCons 1
Regional constraint	o/e 0.84	unconstrained · MANE · 31 kb · p 8.6e-06 · regional, not allelic
Overall
CADD	22.4	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 1.41% European (non-Finnish) · 16,681/1,179,894 alleles

Filtering AF 1.4% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.39%

Overall 1.15% 18,611/1,613,642 alleles · low-frequency

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	1.41%	71
Remaining individualsnot grpmax-eligible	0.965%	104
Middle Eastern	0.792%	126
Admixed American	0.741%	135
Ashkenazi Jewishnot grpmax-eligible	0.389%	257
Finnishnot grpmax-eligible	0.341%	293
South Asian	0.337%	297
Amishnot grpmax-eligible	0.329%	304
African / African-American	0.257%	389

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: DBF4
Protein: p.Lys579Glu
Coding: c.1735A>G
MANE Select: NM_006716
dbSNP: rs61747462
Type: single nucleotide variant
Location: chr7:87907873 (GRCh38)
Gene constraint: LOEUF 0.475 · pLI 0.99 (gnomAD)
Structure: AlphaFold pLDDT 55.17 · 7 PDB

Full DBF4 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DBF4 p.Ile18= Benign ★★ same type
DBF4 p.Ala661Val Uncertain significance ★ ⚠ same type
DBF4 p.Arg101Gln Uncertain significance ★ ⚠ same type
DBF4 p.Arg214Lys Uncertain significance ★ ⚠ same type
DBF4 p.Arg26Gly Uncertain significance ★ ⚠ same type
DBF4 p.Arg576Gln Uncertain significance ★ ⚠ same type
DBF4 p.Arg599Gly Uncertain significance ★ ⚠ same type
DBF4 p.Asn317Ser 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/dbf4-p-lys579glu (accessed [today's date]).

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