Is SLC6A8 p.Pro43= (c.129C>A) pathogenic?

SLC6A8 p.Pro43= (c.129C>A) is classified Likely benign in SLC6A8 (ClinVar, Single submitter, 1 submitter; last evaluated 2020-05-05). No allele count reported in gnomAD v4.1 (AN 1,125,384); Associated with creatine transporter deficiency.

What condition is associated with SLC6A8 p.Pro43= (c.129C>A)?

SLC6A8 p.Pro43= (c.129C>A) is associated with creatine transporter deficiency (ClinVar).

How common is SLC6A8 p.Pro43= (c.129C>A) in the general population?

SLC6A8 p.Pro43= (c.129C>A) is no allele count reported in gnomAD v4.1 (AN 1,125,384) (gnomAD).

How is X-linked creatine transporter deficiency inherited?

Typically Not applicable, X-linked recessive (Orphanet). A genetic counselor can assess individual risk for a family.

SLC6A8 p.Pro43=

c.129C>A · rs782267694 · VCV1104125

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 1,125,384)

Conditions

creatine transporter deficiency

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 -3.2	GERP -2.5
Overall
CADD	7.474	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,125,384). 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: SLC6A8
Protein: p.Pro43=
Coding: c.129C>A
MANE Select: NM_005629
dbSNP: rs782267694
Type: single nucleotide variant
Location: chrX:153688703 (GRCh38)
Structure: AlphaFold pLDDT 85.63 · 6 PDB

Full SLC6A8 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

creatine transporter deficiency — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For X-linked creatine transporter deficiency (Orphanet):

Inheritance: Not applicable, X-linked recessive
Onset: Childhood, Infancy

Similar variants

SLC6A8 p.Pro43Ser Uncertain significance ★★ ⚠ same residue
SLC6A8 c.1016+2T>C Pathogenic ★★★ same condition
SLC6A8 c.1142-2A>G Likely pathogenic ★★★ same condition
SLC6A8 c.1495+2T>G Pathogenic ★★★ same condition
SLC6A8 c.1495+5G>C Pathogenic ★★★ same condition
SLC6A8 c.262+1G>T Pathogenic ★★★ same condition
SLC6A8 c.263-1G>C Pathogenic ★★★ same condition
SLC6A8 c.263-2A>G Pathogenic ★★★ 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/slc6a8-p-pro43 (accessed [today's date]).

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