Is HPD p.Ser177Arg (c.531T>A) pathogenic?

HPD p.Ser177Arg (c.531T>A) is classified Uncertain significance in HPD (ClinVar, Single submitter, 1 submitter; last evaluated 2026-02-01). AlphaMissense: likely benign (0.1556); Very rare (popmax 8.48e-05%, nfe).

How common is HPD p.Ser177Arg (c.531T>A) in the general population?

HPD p.Ser177Arg (c.531T>A) is very rare (popmax 8.48e-05%, nfe) (gnomAD).

What do computational predictors say about HPD p.Ser177Arg (c.531T>A)?

AlphaMissense predicts likely benign (score 0.1556) — an in-silico prediction, not a clinical call.

HPD p.Ser177Arg

c.531T>A · VCV4823447

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1556 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 8.48e-05%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1556	likely benign
REVEL	0.152	moderately benign-leaning
SaProt	LLR -8.60	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 -0.54	GERP -3.9
Regional constraint	o/e 0.87	unconstrained · MANE · 19 kb · p 0.004 · regional, not allelic
Overall
CADD	4.249	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

Grpmax group 8.48e-05% European (non-Finnish) · 1/1,179,684 alleles

Overall 6.84e-05% 1/1,461,512 alleles · very rare

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: HPD
Protein: p.Ser177Arg
Coding: c.531T>A
MANE Select: NM_002150
Type: single nucleotide variant
Location: chr12:121849064 (GRCh38)
Gene constraint: LOEUF 0.845 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 96.00 · 4 PDB

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

Similar variants

HPD p.Ser177= Likely benign ★★ same residue
HPD p.Arg225Ter Pathogenic/Likely pathogenic ★★ same type
HPD p.Gln205Ter Pathogenic/Likely pathogenic ★★ same type
HPD p.Tyr160Cys Likely pathogenic ★★ same type
HPD c.198+3G>A Uncertain significance ★★ same type
HPD p.Ala230Thr Uncertain significance ★★ ⚠ same type
HPD p.Arg111Trp Uncertain significance ★★ ⚠ same type
HPD p.Arg119Gln 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/hpd-p-ser177arg (accessed [today's date]).

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