Is SLC5A7 p.Val63= (c.189C>A) pathogenic?

SLC5A7 p.Val63= (c.189C>A) is classified Uncertain significance in SLC5A7 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-10-30). Absent from gnomAD v4.1; Associated with congenital myasthenic syndrome 20.

What condition is associated with SLC5A7 p.Val63= (c.189C>A)?

SLC5A7 p.Val63= (c.189C>A) is associated with congenital myasthenic syndrome 20, neuronopathy, distal hereditary motor, type 7A (ClinVar).

How common is SLC5A7 p.Val63= (c.189C>A) in the general population?

SLC5A7 p.Val63= (c.189C>A) is absent from gnomAD v4.1 (gnomAD).

SLC5A7 p.Val63=

c.189C>A · VCV3752544

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,611,354)

Conditions

congenital myasthenic syndrome 20

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal.
Splicing
SpliceAI	Δ0.37	acceptor loss, 10 bp away · masked 0 · deltas
Pangolin	Δ0.46	loss · gain 0.01 · agrees with SpliceAI · independent
Constraint at this position
Conservation	phyloP -1.7	GERP -4.1
Overall
CADD	0.312	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,611,354). 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: SLC5A7
Protein: p.Val63=
Coding: c.189C>A
MANE Select: NM_021815
Type: single nucleotide variant
Location: chr2:107992116 (GRCh38)
Gene constraint: LOEUF 0.462 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 84.35 · 12 PDB

Full SLC5A7 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

congenital myasthenic syndrome 20 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: neuronopathy, distal hereditary motor, type 7A

Similar variants

SLC5A7 c.895+1G>C Likely pathogenic ★★ same condition
SLC5A7 c.178+4C>G Uncertain significance ★★ same condition
SLC5A7 c.178+6T>C Uncertain significance ★★ same condition
SLC5A7 c.293-10T>C Uncertain significance ★★ same condition
SLC5A7 c.895+4A>G Uncertain significance ★★ same condition
SLC5A7 p.Ala134Val Uncertain significance ★★ ⚠ same condition
SLC5A7 p.Ala143Thr Uncertain significance ★★ ⚠ same condition
SLC5A7 p.Ala222Val 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/slc5a7-p-val63 (accessed [today's date]).

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