Is FGD1 p.Phe873= (c.2619C>T) pathogenic?

FGD1 p.Phe873= (c.2619C>T) is classified Benign/Likely benign in FGD1 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2026-01-15). Ultra-rare (popmax 0.014%, afr); Associated with Inborn genetic diseases.

What condition is associated with FGD1 p.Phe873= (c.2619C>T)?

FGD1 p.Phe873= (c.2619C>T) is associated with Inborn genetic diseases (ClinVar).

How common is FGD1 p.Phe873= (c.2619C>T) in the general population?

FGD1 p.Phe873= (c.2619C>T) is ultra-rare (popmax 0.014%, afr) (gnomAD).

FGD1 p.Phe873=

c.2619C>T · rs375328916 · VCV585860

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.014%, afr)

Conditions

Inborn genetic diseases

⚠ 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 0.22	GERP -4, phastCons 0.28
Overall
CADD	1.767	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.014% African / African-American · 8/57,316 alleles

Filtering AF 0.00688% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00502%

Overall 0.00141% 17/1,209,196 alleles · ultra-rare exomes 11/1,096,881 · genomes 6/112,315 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.014%	7,165
South Asian	0.00709%	14,103
Admixed American	0.00656%	15,255
East Asian	0.00296%	33,732
European (non-Finnish)	0.000112%	894,775

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: FGD1
Protein: p.Phe873=
Coding: c.2619C>T
MANE Select: NM_004463
dbSNP: rs375328916
Type: single nucleotide variant
Location: chrX:54446376 (GRCh38)

Full FGD1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

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/fgd1-p-phe873 (accessed [today's date]).

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