SLC30A9 p.Pro3=

Q: Is SLC30A9 p.Pro3= (c.9C>G) pathogenic?

SLC30A9 p.Pro3= (c.9C>G) is classified Benign in SLC30A9 (ClinVar, Multiple submitters, 4 submitters; last evaluated 2024-11-26). Common (popmax 96.8%, eas) — too common for a highly-penetrant pathogenic allele; Associated with psychomotor regression-oculomotor apraxia-movement disorder-nephropathy syndrome.

Q: What condition is associated with SLC30A9 p.Pro3= (c.9C>G)?

SLC30A9 p.Pro3= (c.9C>G) is associated with psychomotor regression-oculomotor apraxia-movement disorder-nephropathy syndrome (ClinVar).

Q: How common is SLC30A9 p.Pro3= (c.9C>G) in the general population?

SLC30A9 p.Pro3= (c.9C>G) is common (popmax 96.8%, eas) — too common for a highly-penetrant pathogenic allele (gnomAD).

Q: How is Psychomotor regression-oculomotor apraxia-movement disorder-nephropathy syndrome inherited?

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

c.9C>G · rs2581434 · VCV1242979

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Common

common (popmax 96.8%, eas) — too common for a highly-penetrant pathogenic allele

Conditions

psychomotor regression-oculomotor apraxia-movement disorder-nephropathy syndrome

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 3	GERP -1.2, phastCons 1
Overall
CADD	12.51	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 96.8% East Asian · 43,159/44,572 alleles

Filtering AF 96.1% ClinGen BA1/BS1 input FAF95, joint · FAF99 95.7%

Overall 80.7% 1,293,639/1,602,308 alleles · common exomes 1,188,670/1,450,030 · genomes 104,969/152,278 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	96.8%	1
Amishnot grpmax-eligible	91.7%	1
South Asian	86.3%	1
Admixed American	83.5%	1
Finnishnot grpmax-eligible	82.7%	1
European (non-Finnish)	82.6%	1
Ashkenazi Jewishnot grpmax-eligible	79.8%	1
Remaining individualsnot grpmax-eligible	79.5%	1
Middle Eastern	77.1%	1
African / African-American	32.4%	3

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: SLC30A9
Protein: p.Pro3=
Coding: c.9C>G
MANE Select: NM_006345
dbSNP: rs2581434
Type: single nucleotide variant
Location: chr4:41990660 (GRCh38)
Gene constraint: LOEUF 0.587 · pLI 0.84 (gnomAD)
Structure: AlphaFold pLDDT 75.06 · 1 PDB

Full SLC30A9 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

psychomotor regression-oculomotor apraxia-movement disorder-nephropathy syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Psychomotor regression-oculomotor apraxia-movement disorder-nephropathy syndrome (Orphanet):

Inheritance: Autosomal recessive
Onset: Infancy

Similar variants

SLC30A9 c.274+38C>G Benign ★★ same condition
SLC30A9 c.527+35A>G Benign ★★ same condition
SLC30A9 p.Gly122= Benign ★★ same condition
SLC30A9 p.Met50Val Benign ★★ same condition
SLC30A9 p.Thr97Ala Benign ★★ same condition
SLC30A9 c.840+1G>A Likely pathogenic ★ same condition
SLC30A9 c.841-1G>A Likely pathogenic ★ same condition
SLC30A9 p.Ser438Ter Likely 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/slc30a9-p-pro3 (accessed [today's date]).

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