Is SLC18A3 p.Pro144Ser (c.430C>T) pathogenic?

SLC18A3 p.Pro144Ser (c.430C>T) is classified Uncertain significance in SLC18A3 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-12-03). AlphaMissense: likely benign (0.122); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with SLC18A3 p.Pro144Ser (c.430C>T)?

SLC18A3 p.Pro144Ser (c.430C>T) is associated with Inborn genetic diseases (ClinVar).

How common is SLC18A3 p.Pro144Ser (c.430C>T) in the general population?

SLC18A3 p.Pro144Ser (c.430C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about SLC18A3 p.Pro144Ser (c.430C>T)?

AlphaMissense predicts likely benign (score 0.122) — an in-silico prediction, not a clinical call.

SLC18A3 p.Pro144Ser

c.430C>T · VCV4631045

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.122 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.122	likely benign
REVEL	0.048	moderately benign-leaning
SaProt	LLR -11.65	damaging
⇒ SaProt calls this damaging; AlphaMissense and REVEL do not.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 0.99	GERP -1.5, phastCons 0.74
Regional constraint	o/e 1.00	unconstrained · MANE · 1,196 bp · p 0.99 · regional, not allelic
Overall
CADD	16.33	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

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: SLC18A3
Protein: p.Pro144Ser
Coding: c.430C>T
MANE Select: NM_020549 · reported on NM_003055
Type: single nucleotide variant
Location: chr10:49611170 (GRCh38)

Full SLC18A3 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

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/slc18a3-p-pro144ser (accessed [today's date]).

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