Is PIGB p.Phe511= (c.1533C>T) pathogenic?

PIGB p.Phe511= (c.1533C>T) is classified Likely benign in PIGB (ClinVar, Single submitter, 1 submitter; last evaluated 2023-10-23). Very rare (popmax 0.00169%, amr).

How common is PIGB p.Phe511= (c.1533C>T) in the general population?

PIGB p.Phe511= (c.1533C>T) is very rare (popmax 0.00169%, amr) (gnomAD).

PIGB p.Phe511=

c.1533C>T · rs879775251 · VCV2708094

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00169%, amr)

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 2.7	GERP 4.6, phastCons 1
Overall
CADD	8.076	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00169% Admixed American · 1/59,144 alleles

Overall 0.000187% 3/1,608,428 alleles · very rare exomes 3/1,456,144 · genomes 0/152,284 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00169%	59,144
Remaining individualsnot grpmax-eligible	0.00161%	62,284
European (non-Finnish)	8.5e-05%	1,177,020

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: PIGB
Protein: p.Phe511=
Coding: c.1533C>T
MANE Select: NM_004855
dbSNP: rs879775251
Type: single nucleotide variant
Location: chr15:55355300 (GRCh38)

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

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/pigb-p-phe511 (accessed [today's date]).

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