Is SLC19A3 p.Phe25Leu (c.75C>A) pathogenic?

SLC19A3 p.Phe25Leu (c.75C>A) is classified Uncertain significance in SLC19A3 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-10-01). AlphaMissense: likely pathogenic (0.7112); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with SLC19A3 p.Phe25Leu (c.75C>A)?

SLC19A3 p.Phe25Leu (c.75C>A) is associated with Inborn genetic diseases (ClinVar).

How common is SLC19A3 p.Phe25Leu (c.75C>A) in the general population?

SLC19A3 p.Phe25Leu (c.75C>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about SLC19A3 p.Phe25Leu (c.75C>A)?

AlphaMissense predicts likely pathogenic (score 0.7112) — an in-silico prediction, not a clinical call.

SLC19A3 p.Phe25Leu

c.75C>A · VCV4631054

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.7112 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL indeterminate

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.7112	likely pathogenic
REVEL	0.557	indeterminate
SaProt	LLR -10.29	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL is indeterminate.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 6.7	GERP 1.9, phastCons 1
Regional constraint	o/e 0.99	unconstrained · MANE · 15 kb · p 0.85 · regional, not allelic
Overall
CADD	26.3	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — 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

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: SLC19A3
Protein: p.Phe25Leu
Coding: c.75C>A
MANE Select: NM_025243
Type: single nucleotide variant
Location: chr2:227702244 (GRCh38)
Gene constraint: LOEUF 0.968 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 81.96 · 19 PDB
Residue 25: an α-helix

Full SLC19A3 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

SLC19A3 p.Ala288Thr Uncertain significance ★★ ⚠ same condition
SLC19A3 p.Ala307Pro Uncertain significance ★★ same condition
SLC19A3 p.Asn340Ser Uncertain significance ★★ ⚠ same condition
SLC19A3 p.Gly154Glu Uncertain significance ★★ ⚠ same condition
SLC19A3 p.Leu177Ser Uncertain significance ★★ ⚠ same condition
SLC19A3 p.Leu73Phe Uncertain significance ★★ ⚠ same condition
SLC19A3 p.Met421Leu Uncertain significance ★★ ⚠ same condition
SLC19A3 p.Pro133Leu Uncertain significance ★★ ⚠ 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/slc19a3-p-phe25leu (accessed [today's date]).

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