Is GDF2 p.Asp180= (c.540T>C) pathogenic?

GDF2 p.Asp180= (c.540T>C) is classified Likely benign in GDF2 (ClinVar, Single submitter, 1 submitter; last evaluated 2020-04-19). Absent from gnomAD v4.1; Associated with Cardiovascular phenotype.

What condition is associated with GDF2 p.Asp180= (c.540T>C)?

GDF2 p.Asp180= (c.540T>C) is associated with Cardiovascular phenotype (ClinVar).

How common is GDF2 p.Asp180= (c.540T>C) in the general population?

GDF2 p.Asp180= (c.540T>C) is absent from gnomAD v4.1 (gnomAD).

GDF2 p.Asp180=

c.540T>C · rs782598334 · VCV1747372

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

Cardiovascular phenotype

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 -1.1	GERP -4
Overall
CADD	2.098	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: GDF2
Protein: p.Asp180=
Coding: c.540T>C
MANE Select: NM_016204
dbSNP: rs782598334
Type: single nucleotide variant
Location: chr10:47325034 (GRCh38)
Gene constraint: LOEUF 1.208 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 75.79 · 20 PDB

Full GDF2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Cardiovascular phenotype — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

GDF2 p.Ala105Gly Uncertain significance ★★ ⚠ same condition
GDF2 p.Arg333Gln Uncertain significance ★★ ⚠ same condition
GDF2 p.Gly247Val Uncertain significance ★★ ⚠ same condition
GDF2 p.Ala105= Likely benign ★★ same condition
GDF2 p.Ala310= Likely benign ★★ same condition
GDF2 p.Ala365= Likely benign ★★ same condition
GDF2 p.Arg319= Likely benign ★★ same condition
GDF2 p.Asn259Ser Benign/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/gdf2-p-asp180 (accessed [today's date]).

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