Is DIP2B p.Asn982= (c.2946T>C) pathogenic?

DIP2B p.Asn982= (c.2946T>C) is classified Benign in DIP2B (ClinVar, Multiple submitters, 2 submitters; last evaluated 2021-07-30). Common (popmax 32.6%, eas) — too common for a highly-penetrant pathogenic allele; Associated with intellectual disability, FRA12A type.

What condition is associated with DIP2B p.Asn982= (c.2946T>C)?

DIP2B p.Asn982= (c.2946T>C) is associated with intellectual disability, FRA12A type (ClinVar).

DIP2B p.Asn982=

Q: How common is DIP2B p.Asn982= (c.2946T>C) in the general population?

DIP2B p.Asn982= (c.2946T>C) is common (popmax 32.6%, eas) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.2946T>C · rs3803181 · VCV1255502

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Common

common (popmax 32.6%, eas) — too common for a highly-penetrant pathogenic allele

Conditions

intellectual disability, FRA12A type

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 -0.45	GERP -1.1, phastCons 0.17
Overall
CADD	6.509	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 32.6% East Asian · 14,632/44,858 alleles

Filtering AF 32.2% ClinGen BA1/BS1 input FAF95, joint · FAF99 32%

Overall 4.73% 76,352/1,613,966 alleles · common

Ancestry group	Frequency	1 in
East Asiangrpmax	32.6%	3
Admixed American	21%	5
South Asian	16%	6
Ashkenazi Jewishnot grpmax-eligible	6.88%	15
African / African-American	6.3%	16
Remaining individualsnot grpmax-eligible	5.68%	18
Middle Eastern	4.78%	21
Finnishnot grpmax-eligible	4.49%	22
Amishnot grpmax-eligible	2.3%	43
European (non-Finnish)	1.78%	56

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.Asn982=
Coding: c.2946T>C
MANE Select: NM_173602
dbSNP: rs3803181
Type: single nucleotide variant
Location: chr12:50718803 (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

intellectual disability, FRA12A type — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

DIP2B p.Asp501Val Uncertain significance ★★ ⚠ same condition
DIP2B p.Pro513Ser Uncertain significance ★★ ⚠ same condition
DIP2B p.Val584Ile Uncertain significance ★★ ⚠ same condition
DIP2B c.1814-15T>C Benign ★★ same condition
DIP2B c.4355-32A>G Benign ★★ same condition
DIP2B p.Ile1477= Benign ★★ same condition
DIP2B p.Pro1384= Benign/Likely benign ★★ same condition
DIP2B p.Thr639= 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/dip2b-p-asn982 (accessed [today's date]).

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