Is ALPL p.Gly455Ser (c.1363G>A) pathogenic?

ALPL p.Gly455Ser (c.1363G>A) is classified Pathogenic/Likely pathogenic in ALPL (ClinVar, Multiple submitters, 13 submitters; last evaluated 2026-03-12). AlphaMissense: likely benign (0.1823); Very rare (popmax 0.00703%, nfe); Associated with ALPL-related disorder.

What condition is associated with ALPL p.Gly455Ser (c.1363G>A)?

ALPL p.Gly455Ser (c.1363G>A) is associated with ALPL-related disorder, hypophosphatasia, adult hypophosphatasia (ClinVar).

How common is ALPL p.Gly455Ser (c.1363G>A) in the general population?

ALPL p.Gly455Ser (c.1363G>A) is very rare (popmax 0.00703%, nfe) (gnomAD).

What do computational predictors say about ALPL p.Gly455Ser (c.1363G>A)?

AlphaMissense predicts likely benign (score 0.1823) — an in-silico prediction, not a clinical call.

ALPL p.Gly455Ser

c.1363G>A · rs149889416 · VCV371400

Pathogenic/Likely pathogenic Multiple submitters

Classification

Pathogenic/Likely pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 13 submitters

AlphaMissense

likely benign

0.1823 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00703%, nfe)

Missense predictors

2/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

ALPL-related disorder

Computational evidence

Protein change
AlphaMissense	0.1823	likely benign ⚠ discordant with ClinVar
REVEL	0.867	moderately pathogenic-leaning
SaProt	LLR -11.34	damaging
⇒ REVEL and SaProt call this damaging; AlphaMissense does not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 0.68, phastCons 1
Regional constraint	o/e 0.83	unconstrained · MANE · 24 kb · p 6.1e-06 · regional, not allelic
Overall
CADD	29.0	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 0.00703% European (non-Finnish) · 83/1,179,950 alleles

Filtering AF 0.00579% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00533%

Overall 0.00527% 85/1,612,488 alleles · very rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00703%	14,216
Admixed American	0.00167%	60,006
South Asian	0.0011%	91,092

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: ALPL
Protein: p.Gly455Ser
Coding: c.1363G>A
MANE Select: NM_000478
dbSNP: rs149889416
Type: single nucleotide variant
Location: chr1:21577436 (GRCh38)
Gene constraint: LOEUF 0.987 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 93.74 · 5 PDB

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

Disease context

ALPL-related disorder

Also linked: hypophosphatasia adult hypophosphatasia childhood hypophosphatasia infantile hypophosphatasia

Similar variants

ALPL p.Gly455Asp Pathogenic/Likely pathogenic ★★ same residue
ALPL p.Gly455= Likely benign ★★ same residue
ALPL c.1190-2A>T Pathogenic ★★ same condition
ALPL c.182-1G>A Pathogenic/Likely pathogenic ★★ same condition
ALPL c.182-2A>G Pathogenic/Likely pathogenic ★★ same condition
ALPL c.297+1G>A Pathogenic/Likely pathogenic ★★ same condition
ALPL c.298-1G>A Pathogenic ★★ same condition
ALPL c.472+1G>A Pathogenic ★★ 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/alpl-p-gly455ser (accessed [today's date]).

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