Is DAP3 p.Val240Phe (c.718G>T) pathogenic?

DAP3 p.Val240Phe (c.718G>T) is classified Benign in DAP3 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2018-02-20). AlphaMissense: likely benign (0.2733); Low-frequency (popmax 1.99%, afr).

How common is DAP3 p.Val240Phe (c.718G>T) in the general population?

DAP3 p.Val240Phe (c.718G>T) is low-frequency (popmax 1.99%, afr) (gnomAD).

What do computational predictors say about DAP3 p.Val240Phe (c.718G>T)?

AlphaMissense predicts likely benign (score 0.2733) — an in-silico prediction, not a clinical call.

DAP3 p.Val240Phe

c.718G>T · rs57692591 · VCV791112

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.2733 · ACMG-weighted

gnomAD v4.1

Rare

low-frequency (popmax 1.99%, afr)

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.2733	likely benign
REVEL	0.304	indeterminate
SaProt	LLR -7.38	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 6.3	GERP 2, phastCons 1
Regional constraint	o/e 0.95	unconstrained · MANE · 28 kb · p 0.25 · regional, not allelic
Overall
CADD	26.0	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 1.99% African / African-American · 1,492/75,036 alleles

Filtering AF 1.9% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.87%

Overall 0.108% 1,748/1,614,176 alleles · low-frequency

Ancestry group	Frequency	1 in
African / African-Americangrpmax	1.99%	50
Remaining individualsnot grpmax-eligible	0.174%	573
Admixed American	0.142%	706
Middle Eastern	0.0825%	1,212
South Asian	0.045%	2,222
East Asian	0.0201%	4,987
European (non-Finnish)	0.000593%	168,578

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: DAP3
Protein: p.Val240Phe
Coding: c.718G>T
MANE Select: NM_004632
dbSNP: rs57692591
Type: single nucleotide variant
Location: chr1:155729241 (GRCh38)
Gene constraint: LOEUF 0.706 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 85.23 · 86 PDB
Residue 240: a UniProt-annotated variant site (in); an α-helix

Full DAP3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

YY1AP1 c.-151-185G>A Uncertain significance ★★ same type
DAP3 p.Arg20Cys Likely benign ★★ ⚠ same type
YY1AP1 c.-151-68T>C Benign/Likely benign ★★ same type
YY1AP1 c.-30C>T Benign ★★ same type
YY1AP1 c.-49T>C Benign ★★ same type
YY1AP1 c.-60T>C Benign/Likely benign ★★ same type
YY1AP1 c.-95G>A Benign ★★ same type
DAP3 p.Glu392Lys Likely pathogenic ★ ⚠ 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/dap3-p-val240phe (accessed [today's date]).

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