Is GDF1 p.Pro329= (c.987G>A) pathogenic?

GDF1 p.Pro329= (c.987G>A) is classified Likely benign in GDF1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-10-18). Ultra-rare (popmax 0.0176%, mid).

How common is GDF1 p.Pro329= (c.987G>A) in the general population?

GDF1 p.Pro329= (c.987G>A) is ultra-rare (popmax 0.0176%, mid) (gnomAD).

GDF1 p.Pro329=

c.987G>A · rs773271648 · VCV1903448

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0176%, mid)

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -13	GERP -4
Overall
CADD	0.992	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0176% Middle Eastern · 1/5,682 alleles

Filtering AF 0.00521% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0048%

Overall 0.0058% 89/1,535,448 alleles · ultra-rare exomes 72/1,384,232 · genomes 17/151,216 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0176%	5,682
Finnishnot grpmax-eligible	0.0121%	8,233
Remaining individualsnot grpmax-eligible	0.00677%	14,761
European (non-Finnish)	0.00642%	15,587
South Asian	0.00238%	41,946
Admixed American	0.00199%	50,366
African / African-American	0.00138%	72,326

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: GDF1
Protein: p.Pro329=
Coding: c.987G>A
MANE Select: NM_001492
dbSNP: rs773271648
Type: single nucleotide variant
Location: chr19:18868729 (GRCh38)

Full GDF1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

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/gdf1-p-pro329 (accessed [today's date]).

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