Is PANK2 p.Phe362fs (c.1086del) pathogenic?

PANK2 p.Phe362fs (c.1086del) is classified Pathogenic in PANK2 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-11-27). No gnomAD frequency available for this variant; Associated with pantothenate kinase-associated neurodegeneration.

What condition is associated with PANK2 p.Phe362fs (c.1086del)?

PANK2 p.Phe362fs (c.1086del) is associated with pantothenate kinase-associated neurodegeneration (ClinVar).

How common is PANK2 p.Phe362fs (c.1086del) in the general population?

PANK2 p.Phe362fs (c.1086del) is no gnomAD frequency available for this variant (gnomAD).

PANK2 p.Phe362fs

Q: How is Pantothenate kinase-associated neurodegeneration inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

c.1086del · rs2146887806 · VCV1363985

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

pantothenate kinase-associated neurodegeneration

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 5 of 7
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 2.2	GERP 1.9, phastCons 1

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: PANK2
Protein: p.Phe362fs
Coding: c.1086del
MANE Select: NM_001386393
dbSNP: rs2146887806
Type: Deletion
Location: chr20:3916928 (GRCh38)
Gene constraint: LOEUF 1.115 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 73.99 · 1 PDB
Residue 362: a β-strand

Full PANK2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

pantothenate kinase-associated neurodegeneration — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Pantothenate kinase-associated neurodegeneration (Orphanet):

Inheritance: Autosomal recessive
Onset: All ages
Prevalence: 1-9 / 1 000 000 (Europe)

Similar variants

PANK2 p.Arg371_Glu372delinsGln Pathogenic/Likely pathogenic ★★ same condition
PANK2 p.Gly363_Asn364insTer Pathogenic ★★ same condition
PANK2 p.Gly451fs Pathogenic/Likely pathogenic ★★ same condition
PANK2 p.Ser59fs Pathogenic/Likely pathogenic ★★ same condition
PANK2 p.Ser81fs Pathogenic ★★ same condition
PANK2 p.Tyr252fs Pathogenic/Likely pathogenic ★★ same condition
PANK2 c.906-21_906-19del Likely benign ★★ same condition
PANK2 c.906-99_929del 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/pank2-p-phe362fs (accessed [today's date]).

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