Is SLC20A2 p.Glu55fs (c.165_169del) pathogenic?

SLC20A2 p.Glu55fs (c.165169del) is classified Likely pathogenic in SLC20A2 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-08-30). No gnomAD frequency available for this variant; Associated with basal ganglia calcification, idiopathic, 1.

What condition is associated with SLC20A2 p.Glu55fs (c.165_169del)?

SLC20A2 p.Glu55fs (c.165_169del) is associated with basal ganglia calcification, idiopathic, 1 (ClinVar).

How common is SLC20A2 p.Glu55fs (c.165_169del) in the general population?

SLC20A2 p.Glu55fs (c.165_169del) is no gnomAD frequency available for this variant (gnomAD).

How is Bilateral striopallidodentate calcinosis inherited?

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

SLC20A2 p.Glu55fs

c.165_169del · rs2131227624 · VCV1325076

Likely pathogenic Single submitter

Classification

Likely 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

basal ganglia calcification, idiopathic, 1

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 2 of 11
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 9.9	GERP 1.1, 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: SLC20A2
Protein: p.Glu55fs
Coding: c.165_169del
MANE Select: NM_001257180
dbSNP: rs2131227624
Type: Deletion
Location: chr8:42472222 (GRCh38)
Gene constraint: LOEUF 0.644 · pLI 0.02 (gnomAD)
Structure: AlphaFold pLDDT 72.63

Full SLC20A2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

basal ganglia calcification, idiopathic, 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Bilateral striopallidodentate calcinosis (Orphanet):

Inheritance: Autosomal dominant, Autosomal recessive, Not applicable
Onset: Adult

Similar variants

SLC20A2 p.Ile169_Leu170insTer Pathogenic ★★ same condition
SLC20A2 p.Ile285fs Pathogenic/Likely pathogenic ★★ same condition
SLC20A2 p.Ser261fs Pathogenic ★★ same condition
SLC20A2 p.Val195fs Pathogenic/Likely pathogenic ★★ same condition
SLC20A2 c.731-18_738del Pathogenic ★ same condition
SLC20A2 p.Ala21fs Pathogenic ★ same condition
SLC20A2 p.Ala480fs Pathogenic ★ same condition
SLC20A2 p.Asn27fs 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/slc20a2-p-glu55fs (accessed [today's date]).

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