Is OFD1 p.Arg896fs (c.2686_2689del) pathogenic?

OFD1 p.Arg896fs (c.26862689del) is classified Likely pathogenic in OFD1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-07-17). Associated with OFD1-related disorder.

What condition is associated with OFD1 p.Arg896fs (c.2686_2689del)?

OFD1 p.Arg896fs (c.2686_2689del) is associated with OFD1-related disorder (ClinVar).

OFD1 p.Arg896fs

c.2686_2689del · VCV4948967

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

Conditions

OFD1-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a haploinsufficient gene (ClinGen)
NMD	predicted	premature termination codon in exon 20 of 23
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 3.3	GERP 5.1, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Variant & gene context

Gene: OFD1
Protein: p.Arg896fs
Coding: c.2686_2689del
MANE Select: NM_003611
Type: Microsatellite
Location: chrX:13767208 (GRCh38)
Structure: AlphaFold pLDDT 68.41
Residue 896: 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

OFD1-related disorder

Similar variants

OFD1 p.Glu206fs Pathogenic ★★ same condition
TRAPPC2 p.Met81fs Pathogenic ★★ same condition
OFD1 c.655-8A>G Likely pathogenic ★★ same condition
OFD1 p.Arg909Ter Pathogenic/Likely pathogenic ★★ same condition
OFD1 p.Gln966Ter Pathogenic/Likely pathogenic ★★ same condition
TRAPPC2 p.Ser73Leu Pathogenic/Likely pathogenic ★★ same condition
OFD1 p.Asn610Lys Uncertain significance ★★ ⚠ same condition
OFD1 p.Asp371Asn 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-arg896fs (accessed [today's date]).

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