Is DIP2B p.Val269= (c.807C>G) pathogenic?

DIP2B p.Val269= (c.807C>G) is classified Likely benign in DIP2B (ClinVar, No assertion criteria, 1 submitter; last evaluated 2024-03-07). Ultra-rare (popmax 0.0121%, nfe); Associated with DIP2B-related disorder.

What condition is associated with DIP2B p.Val269= (c.807C>G)?

DIP2B p.Val269= (c.807C>G) is associated with DIP2B-related disorder (ClinVar).

How common is DIP2B p.Val269= (c.807C>G) in the general population?

DIP2B p.Val269= (c.807C>G) is ultra-rare (popmax 0.0121%, nfe) (gnomAD).

DIP2B p.Val269=

c.807C>G · VCV3350478

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0121%, nfe)

Conditions

DIP2B-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.4	GERP 0.78, phastCons 1
Overall
CADD	7.385	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0121% European (non-Finnish) · 143/1,178,686 alleles

Filtering AF 0.0105% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00982%

Overall 0.00912% 147/1,611,952 alleles · ultra-rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0121%	8,243
Remaining individualsnot grpmax-eligible	0.00481%	20,777
African / African-American	0.00134%	74,898

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: DIP2B
Protein: p.Val269=
Coding: c.807C>G
MANE Select: NM_173602
Type: single nucleotide variant
Location: chr12:50675339 (GRCh38)
Gene constraint: LOEUF 0.448 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 78.83

Full DIP2B gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

DIP2B-related disorder

Similar variants

DIP2B p.Ala1101Asp Uncertain significance ★ same condition
DIP2B p.Ala1208Ser Uncertain significance ★ ⚠ same condition
DIP2B p.Glu172Ala Uncertain significance ★ ⚠ same condition
DIP2B p.Thr1016Asn Uncertain significance ★ ⚠ same condition
DIP2B p.Ala897Pro Uncertain significance ⚠ same condition
DIP2B p.Asp1565Gly Uncertain significance ⚠ same condition
DIP2B p.Ile792Val Conflicting classifications of pathogenicity ⚠ same condition
DIP2B p.Thr746Arg 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/dip2b-p-val269 (accessed [today's date]).

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