Is RAPSN p.Pro243= (c.729A>G) pathogenic?

RAPSN p.Pro243= (c.729A>G) is classified Likely benign in RAPSN (ClinVar, Single submitter, 1 submitter; last evaluated 2023-08-03). Very rare (popmax 0.00671%, afr); Associated with fetal akinesia deformation sequence 1.

What condition is associated with RAPSN p.Pro243= (c.729A>G)?

RAPSN p.Pro243= (c.729A>G) is associated with fetal akinesia deformation sequence 1, congenital myasthenic syndrome 11 (ClinVar).

How common is RAPSN p.Pro243= (c.729A>G) in the general population?

RAPSN p.Pro243= (c.729A>G) is very rare (popmax 0.00671%, afr) (gnomAD).

RAPSN p.Pro243=

c.729A>G · rs1297914613 · VCV1134757

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00671%, afr)

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	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP -20	GERP -4.1
Overall
CADD	0.152	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00671% African / African-American · 5/74,530 alleles

Filtering AF 0.00256% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00162%

Overall 0.000502% 8/1,594,242 alleles · very rare exomes 5/1,442,708 · genomes 3/151,534 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00671%	14,906
Remaining individualsnot grpmax-eligible	0.00324%	30,899
European (non-Finnish)	8.51e-05%	1,175,206

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.Pro243=
Coding: c.729A>G
MANE Select: NM_005055
dbSNP: rs1297914613
Type: single nucleotide variant
Location: chr11:47441883 (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 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
RAPSN p.Ala142Asp 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-pro243 (accessed [today's date]).

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