Is SLC35A3 p.Val204= (c.612G>A) pathogenic?

SLC35A3 p.Val204= (c.612G>A) is classified Likely benign in SLC35A3 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-10-13). Absent from gnomAD v4.1; Associated with autism spectrum disorder - epilepsy - arthrogryposis syndrome.

What condition is associated with SLC35A3 p.Val204= (c.612G>A)?

SLC35A3 p.Val204= (c.612G>A) is associated with autism spectrum disorder - epilepsy - arthrogryposis syndrome (ClinVar).

How common is SLC35A3 p.Val204= (c.612G>A) in the general population?

SLC35A3 p.Val204= (c.612G>A) is absent from gnomAD v4.1 (gnomAD).

SLC35A3 p.Val204=

Q: How is Autism spectrum disorder-epilepsy-arthrogryposis syndrome inherited?

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

c.612G>A · rs2524558861 · VCV2765481

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,509,174)

Conditions

autism spectrum disorder - epilepsy - arthrogryposis syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.006	GERP -3.3, phastCons 0.26
Overall
CADD	2.074	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,509,174). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: SLC35A3
Protein: p.Val204=
Coding: c.612G>A
MANE Select: NM_012243
dbSNP: rs2524558861
Type: single nucleotide variant
Location: chr1:100011511 (GRCh38)
Gene constraint: LOEUF 1.114 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 89.31

Full SLC35A3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

autism spectrum disorder - epilepsy - arthrogryposis syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Autism spectrum disorder-epilepsy-arthrogryposis syndrome (Orphanet):

Inheritance: Autosomal recessive
Onset: Infancy, Neonatal

Similar variants

SLC35A3 c.342+1G>A Likely pathogenic ★★ same condition
SLC35A3 p.Arg242Ter Pathogenic/Likely pathogenic ★★ same condition
SLC35A3 p.Arg71Ter Pathogenic/Likely pathogenic ★★ same condition
SLC35A3 p.Gln172Ter Pathogenic ★★ same condition
SLC35A3 p.Gly271Ter Pathogenic/Likely pathogenic ★★ same condition
SLC35A3 p.Ser296Gly Pathogenic/Likely pathogenic ★★ ⚠ same condition
SLC35A3 p.Tyr7Ter Pathogenic/Likely pathogenic ★★ same condition
SLC35A3 p.Arg25Cys 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/slc35a3-p-val204 (accessed [today's date]).

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