Is DISP2 p.Asp209= (c.627C>T) pathogenic?

DISP2 p.Asp209= (c.627C>T) is classified Likely benign in DISP2 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-02-01). Rare (popmax 0.867%, afr).

How common is DISP2 p.Asp209= (c.627C>T) in the general population?

DISP2 p.Asp209= (c.627C>T) is rare (popmax 0.867%, afr) (gnomAD).

DISP2 p.Asp209=

c.627C>T · rs75422658 · VCV2645168

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.867%, afr)

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 0.58	GERP 0.27, phastCons 1
Overall
CADD	8.103	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.867% African / African-American · 651/75,056 alleles

Filtering AF 0.812% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.79%

Overall 0.0452% 729/1,614,124 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.867%	115
Remaining individualsnot grpmax-eligible	0.08%	1,250
Admixed American	0.0417%	2,400
South Asian	0.0022%	45,540
European (non-Finnish)	8.47e-05%	1,179,986

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: DISP2
Protein: p.Asp209=
Coding: c.627C>T
MANE Select: NM_033510
dbSNP: rs75422658
Type: single nucleotide variant
Location: chr15:40364861 (GRCh38)
Gene constraint: LOEUF 0.813 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 68.24

Full DISP2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DISP2 p.Pro194= Benign ★★ same type
DISP2 p.Ala1053Thr Uncertain significance ★ ⚠ same type
DISP2 p.Ala1069Gly Uncertain significance ★ ⚠ same type
DISP2 p.Ala1128Ser Uncertain significance ★ ⚠ same type
DISP2 p.Ala1128Val Uncertain significance ★ ⚠ same type
DISP2 p.Ala1210Gly Uncertain significance ★ ⚠ same type
DISP2 p.Ala1343Pro Uncertain significance ★ ⚠ same type
DISP2 p.Ala1343Val Uncertain significance ★ ⚠ 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/disp2-p-asp209 (accessed [today's date]).

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