Is DIP2A p.Ile796= (c.2388C>T) pathogenic?

DIP2A p.Ile796= (c.2388C>T) is classified Benign in DIP2A (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-08-09). Rare (popmax 0.408%, afr); Associated with DIP2A-related disorder.

What condition is associated with DIP2A p.Ile796= (c.2388C>T)?

DIP2A p.Ile796= (c.2388C>T) is associated with DIP2A-related disorder (ClinVar).

How common is DIP2A p.Ile796= (c.2388C>T) in the general population?

DIP2A p.Ile796= (c.2388C>T) is rare (popmax 0.408%, afr) (gnomAD).

DIP2A p.Ile796=

c.2388C>T · rs201630699 · VCV3035876

Benign No assertion criteria

Classification

Benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.408%, afr)

Conditions

DIP2A-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 -6.5	GERP -3.4
Overall
CADD	5.913	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.408% African / African-American · 306/75,058 alleles

Filtering AF 0.37% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.355%

Overall 0.0548% 885/1,613,974 alleles · rare

Ancestry group	Frequency	1 in
Finnishnot grpmax-eligible	0.67%	149
African / African-Americangrpmax	0.408%	245
Middle Eastern	0.033%	3,031
Remaining individualsnot grpmax-eligible	0.032%	3,124
Admixed American	0.0317%	3,159
East Asian	0.0111%	8,974
South Asian	0.011%	9,108
European (non-Finnish)	0.00788%	12,687
Ashkenazi Jewishnot grpmax-eligible	0.00338%	29,602

Finnish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: DIP2A
Protein: p.Ile796=
Coding: c.2388C>T
MANE Select: NM_015151
dbSNP: rs201630699
Type: single nucleotide variant
Location: chr21:46545955 (GRCh38)
Gene constraint: LOEUF 0.617 · pLI <0.01 · ClinGen HI 1/3 (gnomAD)
Structure: AlphaFold pLDDT 78.93

Full DIP2A gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

DIP2A-related disorder

Similar variants

DIP2A p.Ala1026Ser Uncertain significance ★ ⚠ same condition
DIP2A c.2637+25G>T Uncertain significance same condition
DIP2A p.Ala1260Ser Uncertain significance ⚠ same condition
DIP2A p.Arg602Trp Uncertain significance ⚠ same condition
DIP2A p.Glu63Asp Uncertain significance ⚠ same condition
DIP2A p.Lys281Thr Uncertain significance ⚠ same condition
DIP2A p.Ser1249Cys Uncertain significance ⚠ same condition
DIP2A c.1707+7G>A Likely benign 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/dip2a-p-ile796 (accessed [today's date]).

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