Is APOLD1 p.Cys137Ser (c.409T>A) pathogenic?

APOLD1 p.Cys137Ser (c.409T>A) is classified Uncertain significance in APOLD1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-10). AlphaMissense: likely benign (0.2449); Ultra-rare (popmax 0.0165%, mid).

How common is APOLD1 p.Cys137Ser (c.409T>A) in the general population?

APOLD1 p.Cys137Ser (c.409T>A) is ultra-rare (popmax 0.0165%, mid) (gnomAD).

What do computational predictors say about APOLD1 p.Cys137Ser (c.409T>A)?

AlphaMissense predicts likely benign (score 0.2449) — an in-silico prediction, not a clinical call.

APOLD1 p.Cys137Ser

c.409T>A · VCV4127836

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2449 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0165%, mid)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.2449	likely benign
REVEL	0.149	moderately benign-leaning
SaProt	LLR -8.26	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4	GERP 1.6, phastCons 1
Regional constraint	o/e 1.11	unconstrained · MANE · 1,957 bp · p 0.031 · regional, not allelic
Overall
CADD	22.6	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

⚠ Isoform check: AlphaMissense numbered on a different transcript (AM C168S vs ClinVar C137S) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0165% Middle Eastern · 1/6,062 alleles

Overall 0.000137% 2/1,460,878 alleles · ultra-rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0165%	6,062
European (non-Finnish)	8.48e-05%	1,179,906

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: APOLD1
Protein: p.Cys137Ser
Coding: c.409T>A
MANE Select: NM_030817
Type: single nucleotide variant
Location: chr12:12787314 (GRCh38)
Gene constraint: LOEUF 1.959 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 61.17
Residue 137: a UniProt-annotated variant site (in bdvas; likely pathogenic)

Full APOLD1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

APOLD1 p.Ala159Val Uncertain significance ★ ⚠ same type
APOLD1 p.Ala244Thr Uncertain significance ★ ⚠ same type
APOLD1 p.Ala42Pro Uncertain significance ★ ⚠ same type
APOLD1 p.Ala67Ser Uncertain significance ★ ⚠ same type
APOLD1 p.Arg132Leu Uncertain significance ★ ⚠ same type
APOLD1 p.Arg150Leu Uncertain significance ★ ⚠ same type
APOLD1 p.Arg150Ser Uncertain significance ★ ⚠ same type
APOLD1 p.Arg157Lys Uncertain significance ★ ⚠ same type

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/apold1-p-cys137ser (accessed [today's date]).

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