Is PLAUR p.Asp276= (c.828C>T) pathogenic?

PLAUR p.Asp276= (c.828C>T) is classified Likely benign in PLAUR (ClinVar, Single submitter, 1 submitter; last evaluated 2018-03-06). Ultra-rare (popmax 0.0367%, amr).

How common is PLAUR p.Asp276= (c.828C>T) in the general population?

PLAUR p.Asp276= (c.828C>T) is ultra-rare (popmax 0.0367%, amr) (gnomAD).

PLAUR p.Asp276=

c.828C>T · rs531179636 · VCV728077

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0367%, amr)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -1.4	GERP -3.4
Overall
CADD	2.09	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0367% Admixed American · 22/60,024 alleles

Filtering AF 0.0248% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0209%

Overall 0.00186% 30/1,614,208 alleles · ultra-rare exomes 28/1,461,878 · genomes 2/152,330 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0367%	2,728
East Asian	0.00668%	14,963
African / African-American	0.00133%	75,056
European (non-Finnish)	0.000339%	295,006

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: PLAUR
Protein: p.Asp276=
Coding: c.828C>T
MANE Select: NM_002659
dbSNP: rs531179636
Type: single nucleotide variant
Location: chr19:43649070 (GRCh38)
Gene constraint: LOEUF 0.911 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 81.56 · 13 PDB
Residue 276: the upar/ly6 3 domain; an α-helix

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-asp276 (accessed [today's date]).

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