Is SLC35A2 p.Arg34= (c.102C>T) pathogenic?

SLC35A2 p.Arg34= (c.102C>T) is classified Likely benign in SLC35A2 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2026-01-13). Very rare (popmax 0.00201%, nfe); Associated with SLC35A2-congenital disorder of glycosylation.

What condition is associated with SLC35A2 p.Arg34= (c.102C>T)?

SLC35A2 p.Arg34= (c.102C>T) is associated with SLC35A2-congenital disorder of glycosylation (ClinVar).

How common is SLC35A2 p.Arg34= (c.102C>T) in the general population?

SLC35A2 p.Arg34= (c.102C>T) is very rare (popmax 0.00201%, nfe) (gnomAD).

How is SLC35A2-CDG inherited?

Typically Unknown (Orphanet). A genetic counselor can assess individual risk for a family.

SLC35A2 p.Arg34=

c.102C>T · rs977233420 · VCV474045

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00201%, nfe)

Conditions

SLC35A2-congenital disorder of glycosylation

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 4.7	GERP 0.91, phastCons 1
Overall
CADD	12.55	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00201% European (non-Finnish) · 18/893,350 alleles

Filtering AF 0.00126% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00104%

Overall 0.00157% 19/1,206,637 alleles · very rare exomes 18/1,094,353 · genomes 1/112,284 · joint denominator

Ancestry group	Frequency	1 in
Remaining individualsnot grpmax-eligible	0.00211%	47,462
European (non-Finnish)grpmax	0.00201%	49,631

Remaining individuals shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: SLC35A2
Protein: p.Arg34=
Coding: c.102C>T
MANE Select: NM_005660
dbSNP: rs977233420
Type: single nucleotide variant
Location: chrX:48909986 (GRCh38)
Structure: AlphaFold pLDDT 80.59

Full SLC35A2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

SLC35A2-congenital disorder of glycosylation — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For SLC35A2-CDG (Orphanet):

Inheritance: Unknown
Onset: Infancy, Neonatal

Similar variants

SLC35A2 p.Arg34His Uncertain significance ★ ⚠ same residue
SLC35A2 p.Arg34Leu Uncertain significance ★ ⚠ same residue
SLC35A2 p.Arg34Ser Uncertain significance ★ ⚠ same residue
SLC35A2 p.Gly282Arg Pathogenic ★★ same condition
SLC35A2 p.Met1Val Pathogenic/Likely pathogenic ★★ same condition
SLC35A2 p.Tyr267Cys Likely pathogenic ★★ same condition
SLC35A2 p.Val331Ile Pathogenic ★★ same condition
SLC35A2 p.Ala11Ser 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/slc35a2-p-arg34 (accessed [today's date]).

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