Is RAPSN p.Val32= (c.96G>T) pathogenic?

RAPSN p.Val32= (c.96G>T) is classified Likely benign in RAPSN (ClinVar, Single submitter, 1 submitter; last evaluated 2022-12-26). Very rare (popmax 0.0011%, sas); Associated with fetal akinesia deformation sequence 1.

What condition is associated with RAPSN p.Val32= (c.96G>T)?

RAPSN p.Val32= (c.96G>T) is associated with fetal akinesia deformation sequence 1, congenital myasthenic syndrome 11 (ClinVar).

How common is RAPSN p.Val32= (c.96G>T) in the general population?

RAPSN p.Val32= (c.96G>T) is very rare (popmax 0.0011%, sas) (gnomAD).

RAPSN p.Val32=

c.96G>T · rs2076432156 · VCV1674823

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.0011%, sas)

Conditions

fetal akinesia deformation sequence 1

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 -0.099	GERP -4.6, phastCons 0.47
Overall
CADD	7.177	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0011% South Asian · 1/91,088 alleles

Overall 6.19e-05% 1/1,614,232 alleles · very rare exomes 1/1,461,880 · genomes 0/152,352 · joint denominator

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: RAPSN
Protein: p.Val32=
Coding: c.96G>T
MANE Select: NM_005055
dbSNP: rs2076432156
Type: single nucleotide variant
Location: chr11:47448869 (GRCh38)
Gene constraint: LOEUF 1.092 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 93.29

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

Disease context

fetal akinesia deformation sequence 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: congenital myasthenic syndrome 11

Similar variants

RAPSN p.Val32fs Pathogenic ★ same residue
RAPSN c.1166+1G>T Pathogenic/Likely pathogenic ★★ same condition
RAPSN c.192+2T>G Pathogenic ★★ same condition
RAPSN c.531+1G>A Pathogenic/Likely pathogenic ★★ same condition
RAPSN c.531+1G>T Pathogenic/Likely pathogenic ★★ same condition
RAPSN c.913-1G>C Likely pathogenic ★★ same condition
RAPSN c.-199C>G Pathogenic/Likely pathogenic ★★ same condition
RAPSN c.-210A>G Pathogenic/Likely 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/rapsn-p-val32 (accessed [today's date]).

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