Is P4HB p.Asp24= (c.72C>T) pathogenic?

P4HB p.Asp24= (c.72C>T) is classified Likely benign in P4HB (ClinVar, Single submitter, 1 submitter; last evaluated 2025-06-17). No allele count reported in gnomAD v4.1 (AN 1,457,924).

How common is P4HB p.Asp24= (c.72C>T) in the general population?

P4HB p.Asp24= (c.72C>T) is no allele count reported in gnomAD v4.1 (AN 1,457,924) (gnomAD).

P4HB p.Asp24=

c.72C>T · VCV4797351

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,457,924)

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 2.7	GERP 0.92, phastCons 1
Overall
CADD	12.91	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,457,924). 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: P4HB
Protein: p.Asp24=
Coding: c.72C>T
MANE Select: NM_000918
Type: single nucleotide variant
Location: chr17:81860400 (GRCh38)
Gene constraint: LOEUF 0.561 · pLI 0.65 (gnomAD)
Structure: AlphaFold pLDDT 88.62 · 14 PDB
Residue 24: the thioredoxin 1 domain

Full P4HB gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

P4HB p.Asp24Asn Uncertain significance ★ ⚠ same residue
P4HB p.Cys400Arg Likely pathogenic ★★ same type
P4HB p.Arg452Lys Uncertain significance ★★ ⚠ same type
P4HB p.Arg78Thr Uncertain significance ★★ same type
P4HB p.Asn189Ser Uncertain significance ★★ ⚠ same type
P4HB p.Asp365Glu Uncertain significance ★★ ⚠ same type
P4HB p.Cys400Tyr Uncertain significance ★★ ⚠ same type
P4HB p.Gln475Arg 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/p4hb-p-asp24 (accessed [today's date]).

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