Is ARSI p.Ser403= (c.1209C>G) pathogenic?

ARSI p.Ser403= (c.1209C>G) is classified Benign in ARSI (ClinVar, Single submitter, 1 submitter; last evaluated 2025-09-02). Rare (popmax 0.381%, sas); Associated with Spastic paraplegia.

What condition is associated with ARSI p.Ser403= (c.1209C>G)?

ARSI p.Ser403= (c.1209C>G) is associated with Spastic paraplegia (ClinVar).

How common is ARSI p.Ser403= (c.1209C>G) in the general population?

ARSI p.Ser403= (c.1209C>G) is rare (popmax 0.381%, sas) (gnomAD).

ARSI p.Ser403=

c.1209C>G · rs151025550 · VCV465193

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.381%, sas)

Conditions

Spastic paraplegia

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 0.79	GERP -3.7, phastCons 1
Overall
CADD	4.83	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.381% South Asian · 347/91,040 alleles

Filtering AF 0.348% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.335%

Overall 0.218% 3,512/1,613,342 alleles · rare

Ancestry group	Frequency	1 in
Amishnot grpmax-eligible	3.85%	26
South Asiangrpmax	0.381%	262
European (non-Finnish)	0.241%	415
Finnishnot grpmax-eligible	0.191%	523
Remaining individualsnot grpmax-eligible	0.176%	568
Admixed American	0.0566%	1,765
Middle Eastern	0.0495%	2,021
African / African-American	0.024%	4,171
Ashkenazi Jewishnot grpmax-eligible	0.0101%	9,867
East Asian	0.00223%	44,874

Amish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: ARSI
Protein: p.Ser403=
Coding: c.1209C>G
MANE Select: NM_001012301
dbSNP: rs151025550
Type: single nucleotide variant
Location: chr5:150297715 (GRCh38)
Gene constraint: LOEUF 1.403 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 87.35

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

Disease context

Spastic paraplegia — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

ARSI p.Ala216Thr Uncertain significance ★★ ⚠ same condition
ARSI p.Ala259Val Uncertain significance ★★ ⚠ same condition
ARSI p.Ala264Thr Uncertain significance ★★ ⚠ same condition
ARSI p.Ala399Asp Uncertain significance ★★ ⚠ same condition
ARSI p.Ala414Ser Uncertain significance ★★ ⚠ same condition
ARSI p.Ala414Thr Uncertain significance ★★ ⚠ same condition
ARSI p.Ala78Thr Uncertain significance ★★ ⚠ same condition
ARSI p.Arg117Cys 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/arsi-p-ser403 (accessed [today's date]).

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