Is P4HTM p.Pro487Ser (c.1459C>T) pathogenic?

P4HTM p.Pro487Ser (c.1459C>T) is classified Uncertain significance in P4HTM (ClinVar, Single submitter, 1 submitter; last evaluated 2025-11-12). AlphaMissense: likely benign (0.1026); Rare (popmax 0.113%, afr); Associated with Inborn genetic diseases.

What condition is associated with P4HTM p.Pro487Ser (c.1459C>T)?

P4HTM p.Pro487Ser (c.1459C>T) is associated with Inborn genetic diseases (ClinVar).

How common is P4HTM p.Pro487Ser (c.1459C>T) in the general population?

P4HTM p.Pro487Ser (c.1459C>T) is rare (popmax 0.113%, afr) (gnomAD).

What do computational predictors say about P4HTM p.Pro487Ser (c.1459C>T)?

AlphaMissense predicts likely benign (score 0.1026) — an in-silico prediction, not a clinical call.

P4HTM p.Pro487Ser

c.1459C>T · rs200144003 · VCV3207777

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1026 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.113%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.1026	likely benign
REVEL	0.243	benign-leaning
SaProt	LLR -6.53	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 0.05	GERP 0.24, phastCons 0.67
Regional constraint	o/e 0.80	unconstrained · MANE · 17 kb · p 1.5e-07 · regional, not allelic
Overall
CADD	17.94	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 0.113% African / African-American · 85/75,076 alleles

Filtering AF 0.0937% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0866%

Overall 0.00552% 89/1,613,142 alleles · rare exomes 42/1,460,774 · genomes 47/152,368 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.113%	883
Remaining individualsnot grpmax-eligible	0.0032%	31,248
Admixed American	0.00167%	60,036
European (non-Finnish)	8.47e-05%	1,179,990

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: P4HTM
Protein: p.Pro487Ser
Coding: c.1459C>T
MANE Select: NM_177939
dbSNP: rs200144003
Type: single nucleotide variant
Location: chr3:49006857 (GRCh38)
Gene constraint: LOEUF 0.815 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 81.94 · 1 PDB
Residue 487: a UniProt-annotated variant site (in hidea; uncertain significance)

Full P4HTM gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

P4HTM p.Ala233Thr Uncertain significance ★★ ⚠ same condition
P4HTM p.Arg493Gln Uncertain significance ★★ ⚠ same condition
P4HTM p.Ser171Gly Uncertain significance ★★ ⚠ same condition
P4HTM p.Ser184Thr Uncertain significance ★★ ⚠ same condition
P4HTM c.1073+105G>A Uncertain significance ★ same condition
P4HTM c.1073+16C>G Uncertain significance ★ same condition
P4HTM c.1073+36T>G Conflicting classifications of pathogenicity ★ same condition
P4HTM c.1073+38A>G Conflicting classifications of pathogenicity ★ same condition

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/p4htm-p-pro487ser (accessed [today's date]).

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