Is VPS13A p.Phe55fs (c.165del) pathogenic?

VPS13A p.Phe55fs (c.165del) is classified Pathogenic in VPS13A (ClinVar, Single submitter, 1 submitter; last evaluated 2023-07-17). No gnomAD frequency available for this variant.

How common is VPS13A p.Phe55fs (c.165del) in the general population?

VPS13A p.Phe55fs (c.165del) is no gnomAD frequency available for this variant (gnomAD).

VPS13A p.Phe55fs

c.165del · rs2537521721 · VCV2744507

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

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 3 of 72
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.11	GERP -3.6, phastCons 0.12

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: VPS13A
Protein: p.Phe55fs
Coding: c.165del
MANE Select: NM_033305
dbSNP: rs2537521721
Type: Deletion
Location: chr9:77201383 (GRCh38)
Gene constraint: LOEUF 0.696 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Residue 55: the chorein n-terminal domain

Full VPS13A gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

VPS13A c.7157_7172del Pathogenic/Likely pathogenic ★★ same type
VPS13A c.883-1_892del Likely pathogenic ★★ same type
VPS13A p.Ala332fs Pathogenic/Likely pathogenic ★★ same type
VPS13A p.Asn73fs Pathogenic/Likely pathogenic ★★ same type
VPS13A p.Gly3023fs Pathogenic/Likely pathogenic ★★ same type
VPS13A p.Ile1152fs Pathogenic/Likely pathogenic ★★ same type
VPS13A p.Leu466_Tyr467insTer Pathogenic ★★ same type
VPS13A p.Lys1113fs Pathogenic/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/vps13a-p-phe55fs (accessed [today's date]).

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