Is PURB p.Pro161Ser (c.481C>T) pathogenic?

PURB p.Pro161Ser (c.481C>T) is classified Uncertain significance in PURB (ClinVar, Single submitter, 1 submitter; last evaluated 2024-08-05). AlphaMissense: likely benign (0.0576); Absent from gnomAD v4.1.

How common is PURB p.Pro161Ser (c.481C>T) in the general population?

PURB p.Pro161Ser (c.481C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about PURB p.Pro161Ser (c.481C>T)?

AlphaMissense predicts likely benign (score 0.0576) — an in-silico prediction, not a clinical call.

PURB p.Pro161Ser

c.481C>T · VCV3428464

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0576 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0576	likely benign
REVEL	0.059	moderately benign-leaning
SaProt	LLR -6.87	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 7	GERP 0.81, phastCons 1
Regional constraint	o/e 0.78	unconstrained · MANE · 935 bp · p 3.2e-06 · regional, not allelic
Overall
CADD	21.4	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.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: PURB
Protein: p.Pro161Ser
Coding: c.481C>T
MANE Select: NM_033224
Type: single nucleotide variant
Location: chr7:44884868 (GRCh38)
Gene constraint: LOEUF 1.223 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 75.79
Residue 161: the 'dna-binding' region

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

Similar variants

PURB p.Pro161Leu Uncertain significance ★ ⚠ same residue
PURB p.Ala109Asp Uncertain significance ★ ⚠ same type
PURB p.Ala22Val Uncertain significance ★ ⚠ same type
PURB p.Ala271Thr Uncertain significance ★ ⚠ same type
PURB p.Asp89Gly Uncertain significance ★ ⚠ same type
PURB p.Gln20Pro Uncertain significance ★ ⚠ same type
PURB p.Glu127Lys Uncertain significance ★ ⚠ same type
PURB p.Glu199Asp 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/purb-p-pro161ser (accessed [today's date]).

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