Is HPSE p.Phe398Val (c.1192T>G) pathogenic?

HPSE p.Phe398Val (c.1192T>G) is classified Uncertain significance in HPSE (ClinVar, Single submitter, 1 submitter; last evaluated 2025-01-17). AlphaMissense: ambiguous (0.4027); Very rare (popmax 0.00103%, nfe).

How common is HPSE p.Phe398Val (c.1192T>G) in the general population?

HPSE p.Phe398Val (c.1192T>G) is very rare (popmax 0.00103%, nfe) (gnomAD).

What do computational predictors say about HPSE p.Phe398Val (c.1192T>G)?

AlphaMissense predicts ambiguous (score 0.4027) — an in-silico prediction, not a clinical call.

HPSE p.Phe398Val

c.1192T>G · VCV3858617

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.4027 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00103%, nfe)

Missense predictors

0/2 damaging

REVEL, SaProt · AlphaMissense indeterminate

Computational evidence

Protein change
AlphaMissense	0.4027	ambiguous
REVEL	0.25	benign-leaning
SaProt	LLR -9.74	tolerated
⇒ REVEL and SaProt both call this tolerated; AlphaMissense is indeterminate.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 8.9	GERP 1.6, phastCons 1
Regional constraint	o/e 1.01	unconstrained · MANE · 39 kb · p 0.8 · regional, not allelic
Overall
CADD	24.0	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

Grpmax group 0.00103% European (non-Finnish) · 12/1,167,174 alleles

Filtering AF 0.000548% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000433%

Overall 0.00075% 12/1,600,028 alleles · very rare exomes 12/1,447,788 · genomes 0/152,240 · joint denominator

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: HPSE
Protein: p.Phe398Val
Coding: c.1192T>G
MANE Select: NM_001098540
Type: single nucleotide variant
Location: chr4:83306217 (GRCh38)
Gene constraint: LOEUF 1.066 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 95.02 · 58 PDB
Residue 398: the 'required for heterodimerization with the heparanase 8 kda subunit' region

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

Similar variants

HPSE p.Phe398Leu Uncertain significance ★ ⚠ same residue
HPSE c.673+8C>A Benign ★★ same type
HPSE p.Gly370Asp Likely benign ★★ same type
HPSE p.Ala177Gly Uncertain significance ★ ⚠ same type
HPSE p.Ala204Thr Uncertain significance ★ ⚠ same type
HPSE p.Ala285Thr Uncertain significance ★ ⚠ same type
HPSE p.Ala305Thr Uncertain significance ★ ⚠ same type
HPSE p.Ala84Thr 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/hpse-p-phe398val (accessed [today's date]).

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