Is OFD1 p.Phe310Ser (c.929T>C) pathogenic?

OFD1 p.Phe310Ser (c.929T>C) is classified Likely pathogenic in OFD1 (ClinVar, Single submitter, 1 submitter; last evaluated 2013-10-31). AlphaMissense: ambiguous (0.3912); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with OFD1 p.Phe310Ser (c.929T>C)?

OFD1 p.Phe310Ser (c.929T>C) is associated with Inborn genetic diseases (ClinVar).

How common is OFD1 p.Phe310Ser (c.929T>C) in the general population?

OFD1 p.Phe310Ser (c.929T>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about OFD1 p.Phe310Ser (c.929T>C)?

AlphaMissense predicts ambiguous (score 0.3912) — an in-silico prediction, not a clinical call.

OFD1 p.Phe310Ser

c.929T>C · rs797044917 · VCV208732

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.3912 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,134,152)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.3912	ambiguous
REVEL	0.634	indeterminate
SaProt	LLR -9.25	tolerated
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.7	GERP 2.2, phastCons 1
Regional constraint	o/e 0.93	unconstrained · MANE · 25 kb · p 0.12 · regional, not allelic
Overall
CADD	25.7	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,134,152). 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.Phe310Ser
Coding: c.929T>C
MANE Select: NM_003611
dbSNP: rs797044917
Type: single nucleotide variant
Location: chrX:13749527 (GRCh38)
Structure: AlphaFold pLDDT 68.41

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

TRAPPC2 p.Arg35His Uncertain significance ★ ⚠ same condition
TRAPPC2 p.Glu69Gln Uncertain significance ★ ⚠ same condition
TRAPPC2 p.Val8Ile Uncertain significance ★ same condition
OFD1 p.Ile930fs Pathogenic ★★ same condition
OFD1 p.Phe692fs Pathogenic ★ same condition
OFD1 c.1411+1G>A Pathogenic ★★ same type
OFD1 c.2600-1G>C Pathogenic/Likely pathogenic ★★ same type
OFD1 c.655-8A>G Likely 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-phe310ser (accessed [today's date]).

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