Is VPS13B p.Phe55= (c.165C>T) pathogenic?

VPS13B p.Phe55= (c.165C>T) is classified Uncertain significance in VPS13B (ClinVar, No assertion criteria, 1 submitter; last evaluated 2025-03-21). Absent from gnomAD v4.1; Associated with Cohen syndrome.

What condition is associated with VPS13B p.Phe55= (c.165C>T)?

VPS13B p.Phe55= (c.165C>T) is associated with Cohen syndrome (ClinVar).

How common is VPS13B p.Phe55= (c.165C>T) in the general population?

VPS13B p.Phe55= (c.165C>T) is absent from gnomAD v4.1 (gnomAD).

VPS13B p.Phe55=

c.165C>T · VCV4063177

Uncertain significance No assertion criteria

Classification

Uncertain significance

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

Cohen syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal.
Splicing
SpliceAI	Δ0.27	acceptor gain · deltas
Pangolin	Δ0.24	gain · loss 0.06 · agrees with SpliceAI · independent
Constraint at this position
Conservation	phyloP 0.52	GERP -0.41, phastCons 1
Overall
CADD	15.88	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: VPS13B
Protein: p.Phe55=
Coding: c.165C>T
MANE Select: NM_152564
Type: single nucleotide variant
Location: chr8:99038440 (GRCh38)
Gene constraint: LOEUF 0.708 · pLI <0.01 (gnomAD)
Residue 55: the chorein n-terminal domain; a UniProt-annotated variant site (in coh1)

Full VPS13B gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

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

Similar variants

VPS13B p.Phe55fs Pathogenic ★ same residue
VPS13B c.10867+1G>A Likely pathogenic ★★ same condition
VPS13B c.10868-2A>G Likely pathogenic ★★ same condition
VPS13B c.11044+1G>A Pathogenic/Likely pathogenic ★★ same condition
VPS13B c.11392+1G>T Likely pathogenic ★★ same condition
VPS13B c.11496-2A>G Pathogenic ★★ same condition
VPS13B c.11746-1G>A Pathogenic/Likely pathogenic ★★ same condition
VPS13B c.1843+1G>A Likely pathogenic ★★ 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/vps13b-p-phe55 (accessed [today's date]).

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