Is GDF1 p.Arg283= (c.849C>G) pathogenic?

GDF1 p.Arg283= (c.849C>G) is classified Likely benign in GDF1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-11-25). Ultra-rare (popmax 0.0102%, nfe).

How common is GDF1 p.Arg283= (c.849C>G) in the general population?

GDF1 p.Arg283= (c.849C>G) is ultra-rare (popmax 0.0102%, nfe) (gnomAD).

GDF1 p.Arg283=

c.849C>G · rs1200072578 · VCV2739029

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0102%, nfe)

⚠ 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 0.89	GERP -4, phastCons 0.99
Overall
CADD	11.38	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0102% European (non-Finnish) · 111/1,089,766 alleles

Filtering AF 0.00857% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00805%

Overall 0.00777% 112/1,440,902 alleles · ultra-rare exomes 100/1,292,466 · genomes 12/148,436 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0102%	9,818
African / African-American	0.00149%	67,100

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.Arg283=
Coding: c.849C>G
MANE Select: NM_001492
dbSNP: rs1200072578
Type: single nucleotide variant
Location: chr19:18868867 (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-arg283 (accessed [today's date]).

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