Is OFD1 p.Ser660fs (c.1979_1980del) pathogenic?

OFD1 p.Ser660fs (c.19791980del) is classified Pathogenic in OFD1 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2022-02-02). No gnomAD frequency available for this variant; Associated with orofaciodigital syndrome I.

What condition is associated with OFD1 p.Ser660fs (c.1979_1980del)?

OFD1 p.Ser660fs (c.1979_1980del) is associated with orofaciodigital syndrome I (ClinVar).

How common is OFD1 p.Ser660fs (c.1979_1980del) in the general population?

OFD1 p.Ser660fs (c.1979_1980del) is no gnomAD frequency available for this variant (gnomAD).

OFD1 p.Ser660fs

c.1979_1980del · rs312262887 · VCV41089

Pathogenic Multiple submitters

Classification

Pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

orofaciodigital syndrome I

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 -1.1	GERP -1.9

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.Ser660fs
Coding: c.1979_1980del
MANE Select: NM_003611
dbSNP: rs312262887
Type: Microsatellite
Location: chrX:13760437 (GRCh38)
Structure: AlphaFold pLDDT 68.41
Residue 660: the 'mediates homooligomerization' region; the 'mediates the interaction with sdccag8' 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

Similar variants

OFD1 p.Arg205fs Pathogenic/Likely pathogenic ★★ same condition
OFD1 p.Gln398fs Pathogenic ★★ same condition
OFD1 p.Gln423fs Pathogenic ★★ same condition
OFD1 p.Glu206fs Pathogenic ★★ same condition
OFD1 p.Ile930fs Pathogenic ★★ same condition
OFD1 p.Met293fs Pathogenic ★★ same condition
OFD1 p.Glu395del Uncertain significance ★★ same condition
OFD1 p.Glu823del 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-ser660fs (accessed [today's date]).

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