Is DISP3 p.Val296= (c.888C>T) pathogenic?

DISP3 p.Val296= (c.888C>T) is classified Benign in DISP3 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-10-30). Common (popmax 34.5%, afr) — too common for a highly-penetrant pathogenic allele; Associated with DISP3-related disorder.

What condition is associated with DISP3 p.Val296= (c.888C>T)?

DISP3 p.Val296= (c.888C>T) is associated with DISP3-related disorder (ClinVar).

DISP3 p.Val296=

Q: How common is DISP3 p.Val296= (c.888C>T) in the general population?

DISP3 p.Val296= (c.888C>T) is common (popmax 34.5%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.888C>T · rs12144924 · VCV3058907

Benign No assertion criteria

Classification

Benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Common

common (popmax 34.5%, afr) — too common for a highly-penetrant pathogenic allele

Conditions

DISP3-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 0.43	GERP 0.65, phastCons 0.99
Overall
CADD	15.55	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 34.5% African / African-American · 25,894/74,994 alleles

Filtering AF 34.2% ClinGen BA1/BS1 input FAF95, joint · FAF99 34%

Overall 9.04% 145,793/1,612,950 alleles · common

Ancestry group	Frequency	1 in
African / African-Americangrpmax	34.5%	3
South Asian	19.9%	5
Middle Eastern	13.4%	7
Ashkenazi Jewishnot grpmax-eligible	12.1%	8
Finnishnot grpmax-eligible	12.1%	8
Remaining individualsnot grpmax-eligible	9.98%	10
Amishnot grpmax-eligible	8.22%	12
European (non-Finnish)	6.64%	15
Admixed American	5.44%	18
East Asian	4.11%	24

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: DISP3
Protein: p.Val296=
Coding: c.888C>T
MANE Select: NM_020780
dbSNP: rs12144924
Type: single nucleotide variant
Location: chr1:11501880 (GRCh38)
Gene constraint: LOEUF 0.886 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 70.84

Full DISP3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

DISP3-related disorder

Similar variants

DISP3 c.1749+5G>A Likely benign same condition
DISP3 c.3230-4G>A Likely benign same condition
DISP3 p.Ala1000= Likely benign same condition
DISP3 p.Ala1297= Benign same condition
DISP3 p.Ala650Thr Benign same condition
DISP3 p.Arg1022His Likely benign same condition
DISP3 p.Arg166Gln Likely benign same condition
DISP3 p.Arg294= 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/disp3-p-val296 (accessed [today's date]).

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