Is OFD1 p.Phe692fs (c.2076del) pathogenic?

OFD1 p.Phe692fs (c.2076del) is classified Pathogenic in OFD1 (ClinVar, Single submitter, 1 submitter; last evaluated 2015-09-08). Absent from gnomAD; Associated with Inborn genetic diseases.

What condition is associated with OFD1 p.Phe692fs (c.2076del)?

OFD1 p.Phe692fs (c.2076del) is associated with Inborn genetic diseases (ClinVar).

How common is OFD1 p.Phe692fs (c.2076del) in the general population?

OFD1 p.Phe692fs (c.2076del) is absent from gnomAD (gnomAD).

OFD1 p.Phe692fs

c.2076del · rs1555907034 · VCV520748

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

Inborn genetic diseases

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 16 of 23
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -5.2	GERP -7.6

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

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: OFD1
Protein: p.Phe692fs
Coding: c.2076del
MANE Select: NM_003611
dbSNP: rs1555907034
Type: Deletion
Location: chrX:13760532 (GRCh38)
Structure: AlphaFold pLDDT 68.41
Residue 692: the 'mediates the interaction with sdccag8' region

Full OFD1 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

Similar variants

OFD1 p.Phe692Ile Uncertain significance ★ ⚠ same residue
OFD1 p.Phe692Ser Uncertain significance ★ ⚠ same residue
OFD1 p.Ile930fs Pathogenic ★★ same condition
OFD1 p.Phe310Ser Likely pathogenic ★ same condition
TRAPPC2 p.Arg35His Uncertain significance ★ ⚠ same condition
TRAPPC2 p.Glu69Gln Uncertain significance ★ ⚠ same condition
TRAPPC2 p.Val8Ile Uncertain significance ★ same condition
OFD1 p.Arg373fs Pathogenic ★★ same type

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-phe692fs (accessed [today's date]).

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