Is SLC20A2 p.Pro367= (c.1101C>G) pathogenic?

SLC20A2 p.Pro367= (c.1101C>G) is classified Benign/Likely benign in SLC20A2 (ClinVar, Multiple submitters, 4 submitters; last evaluated 2025-06-12). Rare (popmax 0.113%, amr); Associated with basal ganglia calcification, idiopathic, 1.

What condition is associated with SLC20A2 p.Pro367= (c.1101C>G)?

SLC20A2 p.Pro367= (c.1101C>G) is associated with basal ganglia calcification, idiopathic, 1 (ClinVar).

How common is SLC20A2 p.Pro367= (c.1101C>G) in the general population?

SLC20A2 p.Pro367= (c.1101C>G) is rare (popmax 0.113%, amr) (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.Pro367=

c.1101C>G · rs199935692 · VCV911277

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

rare (popmax 0.113%, amr)

Conditions

basal ganglia calcification, idiopathic, 1

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP -9.1	GERP -3.6
Overall
CADD	0.064	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.113% Admixed American · 68/60,010 alleles

Filtering AF 0.0917% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0838%

Overall 0.0137% 221/1,614,094 alleles · rare exomes 170/1,461,888 · genomes 51/152,206 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.113%	883
Middle Eastern	0.0495%	2,021
Remaining individualsnot grpmax-eligible	0.0432%	2,315
European (non-Finnish)	0.0102%	9,834
African / African-American	0.004%	25,006

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: SLC20A2
Protein: p.Pro367=
Coding: c.1101C>G
MANE Select: NM_001257180
dbSNP: rs199935692
Type: single nucleotide variant
Location: chr8:42437411 (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.Pro367Ser Uncertain significance ★ ⚠ same residue
SLC20A2 c.1794+1G>C Pathogenic/Likely pathogenic ★★ same condition
SLC20A2 c.290-8A>G Pathogenic ★★ same condition
SLC20A2 c.935-2A>G Pathogenic ★★ same condition
SLC20A2 p.Arg382Ter Pathogenic ★★ same condition
SLC20A2 p.Arg467Ter Pathogenic ★★ same condition
SLC20A2 p.Asp28Asn Pathogenic/Likely pathogenic ★★ same condition
SLC20A2 p.Gln46Ter 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-pro367 (accessed [today's date]).

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