Is PANK2 p.Asp44= (c.132C>T) pathogenic?

PANK2 p.Asp44= (c.132C>T) is classified Benign/Likely benign in PANK2 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2026-01-20). Ultra-rare (popmax 0.0591%, eas); Associated with pantothenate kinase-associated neurodegeneration.

What condition is associated with PANK2 p.Asp44= (c.132C>T)?

PANK2 p.Asp44= (c.132C>T) is associated with pantothenate kinase-associated neurodegeneration (ClinVar).

How common is PANK2 p.Asp44= (c.132C>T) in the general population?

PANK2 p.Asp44= (c.132C>T) is ultra-rare (popmax 0.0591%, eas) (gnomAD).

PANK2 p.Asp44=

Q: How is Pantothenate kinase-associated neurodegeneration inherited?

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

c.132C>T · rs781106176 · VCV559122

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0591%, eas)

Conditions

pantothenate kinase-associated neurodegeneration

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -0.66	GERP -3.2
Overall
CADD	6.91	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0591% East Asian · 21/35,540 alleles

Filtering AF 0.0395% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0332%

Overall 0.00625% 90/1,439,112 alleles · ultra-rare exomes 78/1,286,834 · genomes 12/152,278 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0591%	1,692
European (non-Finnish)	0.00569%	17,564
Remaining individualsnot grpmax-eligible	0.00541%	18,482
South Asian	0.00432%	23,169

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: PANK2
Protein: p.Asp44=
Coding: c.132C>T
MANE Select: NM_001386393
dbSNP: rs781106176
Type: single nucleotide variant
Location: chr20:3889562 (GRCh38)

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)

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-asp44 (accessed [today's date]).

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