Is OFD1 p.Pro773= (c.2319A>G) pathogenic?

OFD1 p.Pro773= (c.2319A>G) is classified Likely benign in OFD1 (ClinVar, Multiple submitters, 4 submitters; last evaluated 2025-04-07). Ultra-rare (popmax 0.0889%, eas); Associated with orofaciodigital syndrome I.

What condition is associated with OFD1 p.Pro773= (c.2319A>G)?

OFD1 p.Pro773= (c.2319A>G) is associated with orofaciodigital syndrome I, Joubert syndrome, inherited retinal dystrophy (ClinVar).

How common is OFD1 p.Pro773= (c.2319A>G) in the general population?

OFD1 p.Pro773= (c.2319A>G) is ultra-rare (popmax 0.0889%, eas) (gnomAD).

OFD1 p.Pro773=

c.2319A>G · rs752137789 · VCV412875

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0889%, eas)

Conditions

orofaciodigital syndrome I

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 -1.5	GERP -6.2
Overall
CADD	0.186	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0889% East Asian · 30/33,753 alleles

Filtering AF 0.0639% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0555%

Overall 0.00373% 45/1,207,994 alleles · ultra-rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0889%	1,125
Remaining individualsnot grpmax-eligible	0.00421%	23,770
European (non-Finnish)	0.00145%	68,759

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: OFD1
Protein: p.Pro773=
Coding: c.2319A>G
MANE Select: NM_003611
dbSNP: rs752137789
Type: single nucleotide variant
Location: chrX:13761143 (GRCh38)
Structure: AlphaFold pLDDT 68.41
Residue 773: the 'mediates the interaction with sdccag8' region; the 'disordered' region

Full OFD1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

orofaciodigital syndrome I — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: Joubert syndrome inherited retinal dystrophy

Similar variants

OFD1 c.1411+1G>A Pathogenic ★★ same condition
OFD1 c.2600-1G>C Pathogenic/Likely pathogenic ★★ same condition
OFD1 p.Arg367Ter Pathogenic ★★ same condition
OFD1 p.Arg41Ter Pathogenic ★★ same condition
OFD1 p.Arg890Ter Pathogenic/Likely pathogenic ★★ same condition
OFD1 p.Arg909Ter Pathogenic/Likely pathogenic ★★ same condition
OFD1 p.Tyr87Cys Pathogenic ★★ ⚠ same condition
OFD1 c.2388-3T>C Uncertain significance ★★ 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/ofd1-p-pro773 (accessed [today's date]).

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