Is ALPL p.Ile395Val (c.1183A>G) pathogenic?

ALPL p.Ile395Val (c.1183A>G) is classified Pathogenic/Likely pathogenic in ALPL (ClinVar, Multiple submitters, 6 submitters; last evaluated 2026-01-07). AlphaMissense: likely benign (0.1222); Very rare (popmax 0.00667%, amr); Associated with adult hypophosphatasia.

What condition is associated with ALPL p.Ile395Val (c.1183A>G)?

ALPL p.Ile395Val (c.1183A>G) is associated with adult hypophosphatasia, hypophosphatasia, childhood hypophosphatasia (ClinVar).

How common is ALPL p.Ile395Val (c.1183A>G) in the general population?

ALPL p.Ile395Val (c.1183A>G) is very rare (popmax 0.00667%, amr) (gnomAD).

What do computational predictors say about ALPL p.Ile395Val (c.1183A>G)?

AlphaMissense predicts likely benign (score 0.1222) — an in-silico prediction, not a clinical call.

ALPL p.Ile395Val

c.1183A>G · rs772682471 · VCV1452498

Pathogenic/Likely pathogenic Multiple submitters

Classification

Pathogenic/Likely pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 6 submitters

AlphaMissense

likely benign

0.1222 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00667%, amr)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

adult hypophosphatasia

Computational evidence

Protein change
AlphaMissense	0.1222	likely benign ⚠ discordant with ClinVar
REVEL	0.766	pathogenic-leaning
SaProt	LLR -8.34	tolerated
⇒ REVEL calls this damaging; AlphaMissense and SaProt do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 11	GERP 1.6, phastCons 1
Regional constraint	o/e 0.83	unconstrained · MANE · 24 kb · p 6.1e-06 · regional, not allelic
Overall
CADD	22.7	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 0.00667% Admixed American · 4/60,006 alleles

Filtering AF 0.00226% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00135%

Overall 0.000805% 13/1,613,976 alleles · very rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00667%	15,002
East Asian	0.00446%	22,444
Remaining individualsnot grpmax-eligible	0.0016%	62,488
European (non-Finnish)	0.000508%	196,667

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.Ile395Val
Coding: c.1183A>G
MANE Select: NM_000478
dbSNP: rs772682471
Type: single nucleotide variant
Location: chr1:21575918 (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

adult hypophosphatasia — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: hypophosphatasia childhood hypophosphatasia infantile hypophosphatasia

Similar variants

ALPL p.Ile395Thr Pathogenic/Likely pathogenic ★★ same residue
ALPL p.Ile395Phe Conflicting classifications of pathogenicity ★ ⚠ 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-ile395val (accessed [today's date]).

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