Is SLC35B2 p.Pro96Arg (c.287C>G) pathogenic?

SLC35B2 p.Pro96Arg (c.287C>G) is classified Uncertain significance in SLC35B2 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-07-25). AlphaMissense: likely benign (0.1006); Absent from gnomAD v4.1.

How common is SLC35B2 p.Pro96Arg (c.287C>G) in the general population?

SLC35B2 p.Pro96Arg (c.287C>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about SLC35B2 p.Pro96Arg (c.287C>G)?

AlphaMissense predicts likely benign (score 0.1006) — an in-silico prediction, not a clinical call.

SLC35B2 p.Pro96Arg

c.287C>G · rs2534338670 · VCV2613851

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1006 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1006	likely benign
REVEL	0.027	moderately benign-leaning
SaProt	LLR -6.82	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 9.9	GERP 1.5, phastCons 1
Regional constraint	o/e 1.16	unconstrained · MANE · 2,701 bp · p 0.00026 · regional, not allelic
Overall
CADD	22.0	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: SLC35B2
Protein: p.Pro96Arg
Coding: c.287C>G
MANE Select: NM_178148
dbSNP: rs2534338670
Type: single nucleotide variant
Location: chr6:44256415 (GRCh38)
Gene constraint: LOEUF 0.709 · pLI 0.01 (gnomAD)
Structure: AlphaFold pLDDT 81.29

Full SLC35B2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

SLC35B2 p.Phe206= Likely benign ★★ same type
SLC35B2 p.Ala140Thr Uncertain significance ★ ⚠ same type
SLC35B2 p.Ala142Asp Uncertain significance ★ ⚠ same type
SLC35B2 p.Ala142Val Uncertain significance ★ ⚠ same type
SLC35B2 p.Ala19Glu Uncertain significance ★ ⚠ same type
SLC35B2 p.Ala280Val Uncertain significance ★ ⚠ same type
SLC35B2 p.Ala404Gly Uncertain significance ★ ⚠ same type
SLC35B2 p.Ala411Thr Uncertain significance ★ ⚠ 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/slc35b2-p-pro96arg (accessed [today's date]).

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