Is PDF p.Asp72Asn (c.214G>A) pathogenic?

PDF p.Asp72Asn (c.214G>A) is classified Uncertain significance in PDF (ClinVar, Single submitter, 1 submitter; last evaluated 2025-05-21). AlphaMissense: ambiguous (0.5311); No allele count reported in gnomAD v4.1 (AN 1,475,978).

How common is PDF p.Asp72Asn (c.214G>A) in the general population?

PDF p.Asp72Asn (c.214G>A) is no allele count reported in gnomAD v4.1 (AN 1,475,978) (gnomAD).

What do computational predictors say about PDF p.Asp72Asn (c.214G>A)?

AlphaMissense predicts ambiguous (score 0.5311) — an in-silico prediction, not a clinical call.

PDF p.Asp72Asn

c.214G>A · VCV3930150

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.5311 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,475,978)

Missense predictors

0/2 damaging

REVEL, SaProt · AlphaMissense no call

Computational evidence

Protein change
AlphaMissense	0.5311	ambiguous
REVEL	0.229	benign-leaning
SaProt	LLR -9.25	tolerated
⇒ REVEL and SaProt both call this tolerated; AlphaMissense makes no call.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 5.7	GERP 1.5, phastCons 1
Regional constraint	o/e 1.23	unconstrained · MANE · 1,545 bp · p 9e-06 · regional, not allelic
Overall
CADD	25.9	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

No allele count reported in gnomAD v4.1 (AN 1,475,978). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: PDF
Protein: p.Asp72Asn
Coding: c.214G>A
MANE Select: NM_032382 · reported on NM_022341
Type: single nucleotide variant
Location: chr16:69330357 (GRCh38)

Full PDF 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/pdf-p-asp72asn (accessed [today's date]).

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