Is OPLAH p.Val528= (c.1584G>A) pathogenic?

OPLAH p.Val528= (c.1584G>A) is classified Likely benign in OPLAH (ClinVar, Single submitter, 1 submitter; last evaluated 2023-03-12). Ultra-rare (popmax 0.0331%, mid); Associated with 5-oxoprolinase deficiency.

What condition is associated with OPLAH p.Val528= (c.1584G>A)?

OPLAH p.Val528= (c.1584G>A) is associated with 5-oxoprolinase deficiency (ClinVar).

How common is OPLAH p.Val528= (c.1584G>A) in the general population?

OPLAH p.Val528= (c.1584G>A) is ultra-rare (popmax 0.0331%, mid) (gnomAD).

How is 5-oxoprolinase deficiency inherited?

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

OPLAH p.Val528=

c.1584G>A · rs188318488 · VCV2727239

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0331%, mid)

Conditions

5-oxoprolinase deficiency

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
Overall
CADD	0.139	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0331% Middle Eastern · 2/6,036 alleles

Filtering AF 0.00854% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00798%

Overall 0.0083% 133/1,602,676 alleles · ultra-rare exomes 123/1,450,432 · genomes 10/152,244 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0331%	3,018
European (non-Finnish)	0.01%	9,964
Remaining individualsnot grpmax-eligible	0.00644%	15,530
South Asian	0.00562%	17,802
African / African-American	0.004%	24,971
Admixed American	0.00171%	58,404

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: OPLAH
Protein: p.Val528=
Coding: c.1584G>A
MANE Select: NM_017570
dbSNP: rs188318488
Type: single nucleotide variant
Location: chr8:144057070 (GRCh38)
Gene constraint: LOEUF 1.163 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 88.08

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

Disease context

5-oxoprolinase deficiency — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For 5-oxoprolinase deficiency (Orphanet):

Inheritance: Autosomal recessive
Onset: Childhood, Infancy, Neonatal

Similar variants

OPLAH c.587+1G>A Pathogenic/Likely pathogenic ★★ same condition
OPLAH p.Gln1006Ter Pathogenic/Likely pathogenic ★★ same condition
OPLAH p.Tyr248Ter Likely pathogenic ★★ same condition
OPLAH p.Ala1093Val Uncertain significance ★★ ⚠ same condition
OPLAH p.Ala344Thr Uncertain significance ★★ ⚠ same condition
OPLAH p.Ala422Val Uncertain significance ★★ ⚠ same condition
OPLAH p.Ala46Thr Uncertain significance ★★ ⚠ same condition
OPLAH p.Ala475Val Uncertain significance ★★ ⚠ 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/oplah-p-val528 (accessed [today's date]).

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