Is PLAUR p.Ser87Arg (c.261C>A) pathogenic?

PLAUR p.Ser87Arg (c.261C>A) is classified Uncertain significance in PLAUR (ClinVar, Single submitter, 1 submitter; last evaluated 2025-10-07). AlphaMissense: likely pathogenic (0.9364); Very rare (popmax 0.00653%, nfe).

How common is PLAUR p.Ser87Arg (c.261C>A) in the general population?

PLAUR p.Ser87Arg (c.261C>A) is very rare (popmax 0.00653%, nfe) (gnomAD).

What do computational predictors say about PLAUR p.Ser87Arg (c.261C>A)?

AlphaMissense predicts likely pathogenic (score 0.9364) — an in-silico prediction, not a clinical call.

PLAUR p.Ser87Arg

c.261C>A · rs144494060 · VCV2596135

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9364 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00653%, nfe)

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL indeterminate

Computational evidence

Protein change
AlphaMissense	0.9364	likely pathogenic
REVEL	0.298	indeterminate
SaProt	LLR -7.38	tolerated
⇒ AlphaMissense calls this damaging; SaProt does not; REVEL is indeterminate.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.27	GERP 0.96, phastCons 0.96
Regional constraint	o/e 0.94	unconstrained · MANE · 21 kb · p 0.2 · regional, not allelic
Overall
CADD	15.61	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00653% European (non-Finnish) · 77/1,179,980 alleles

Filtering AF 0.0053% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0049%

Overall 0.00521% 84/1,613,778 alleles · very rare exomes 80/1,461,860 · genomes 4/151,918 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00653%	15,324
Remaining individualsnot grpmax-eligible	0.0064%	15,619
African / African-American	0.00401%	24,946

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: PLAUR
Protein: p.Ser87Arg
Coding: c.261C>A
MANE Select: NM_002659
dbSNP: rs144494060
Type: single nucleotide variant
Location: chr19:43665365 (GRCh38)
Gene constraint: LOEUF 0.911 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 81.56 · 13 PDB
Residue 87: the upar/ly6 1 domain; a β-strand

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

Similar variants

PLAUR p.His251= Likely benign ★★ same type
PLAUR p.Met268Val Likely benign ★★ same type
PLAUR p.Pro8= Benign/Likely benign ★★ same type
PLAUR p.Ala106Asp Uncertain significance ★ ⚠ same type
PLAUR p.Arg113Cys Uncertain significance ★ ⚠ same type
PLAUR p.Arg113His Uncertain significance ★ ⚠ same type
PLAUR p.Arg131Gly Uncertain significance ★ ⚠ same type
PLAUR p.Arg164Cys 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/plaur-p-ser87arg (accessed [today's date]).

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