Is SLC16A2 p.Pro382Ser (c.1144C>T) pathogenic?

SLC16A2 p.Pro382Ser (c.1144C>T) is classified Uncertain significance in SLC16A2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-02-05). AlphaMissense: likely benign (0.1741); Absent from gnomAD v4.1.

How common is SLC16A2 p.Pro382Ser (c.1144C>T) in the general population?

SLC16A2 p.Pro382Ser (c.1144C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about SLC16A2 p.Pro382Ser (c.1144C>T)?

AlphaMissense predicts likely benign (score 0.1741) — an in-silico prediction, not a clinical call.

SLC16A2 p.Pro382Ser

c.1144C>T · rs2519807448 · VCV1803323

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1741 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1741	likely benign
REVEL	0.28	benign-leaning
SaProt	LLR -5.80	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 7.6	GERP 2.1, phastCons 1
Regional constraint	o/e 0.66	unconstrained · MANE · 6,945 bp · p 3.2e-07 · regional, not allelic
Overall
CADD	23.6	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

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: SLC16A2
Protein: p.Pro382Ser
Coding: c.1144C>T
MANE Select: NM_006517
dbSNP: rs2519807448
Type: single nucleotide variant
Location: chrX:74525867 (GRCh38)
Structure: AlphaFold pLDDT 79.48 · 7 PDB

Full SLC16A2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

SLC16A2 p.Pro382Leu Uncertain significance ★★ ⚠ same residue
SLC16A2 c.1399+1G>A Pathogenic ★★ same type
SLC16A2 c.576-1G>A Pathogenic/Likely pathogenic ★★ same type
SLC16A2 p.Ala150Val Pathogenic/Likely pathogenic ★★ ⚠ same type
SLC16A2 p.Arg171Ter Pathogenic ★★ same type
SLC16A2 p.Arg314Ter Pathogenic ★★ same type
SLC16A2 p.Arg371Cys Pathogenic/Likely pathogenic ★★ same type
SLC16A2 p.Asp424Asn Likely pathogenic ★★ ⚠ same type

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/slc16a2-p-pro382ser (accessed [today's date]).

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