Is ARSL p.Ser233= (c.699G>A) pathogenic?

ARSL p.Ser233= (c.699G>A) is classified Likely benign in ARSL (ClinVar, Single submitter, 1 submitter; last evaluated 2024-02-06). Ultra-rare (popmax 0.0106%, afr); Associated with chondrodysplasia punctata, brachytelephalangic, autosomal.

What condition is associated with ARSL p.Ser233= (c.699G>A)?

ARSL p.Ser233= (c.699G>A) is associated with chondrodysplasia punctata, brachytelephalangic, autosomal (ClinVar).

How common is ARSL p.Ser233= (c.699G>A) in the general population?

ARSL p.Ser233= (c.699G>A) is ultra-rare (popmax 0.0106%, afr) (gnomAD).

ARSL p.Ser233=

c.699G>A · rs765024303 · VCV3002866

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0106%, afr)

Conditions

chondrodysplasia punctata, brachytelephalangic, autosomal

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 -8.9	GERP -2.9
Overall
CADD	0.49	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0106% African / African-American · 6/56,854 alleles

Filtering AF 0.00807% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00745%

Overall 0.00811% 98/1,208,910 alleles · ultra-rare exomes 91/1,098,242 · genomes 7/110,668 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0106%	9,476
European (non-Finnish)	0.00972%	10,288
Remaining individualsnot grpmax-eligible	0.00631%	15,860
South Asian	0.00353%	28,340

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: ARSL
Protein: p.Ser233=
Coding: c.699G>A
MANE Select: NM_000047
dbSNP: rs765024303
Type: single nucleotide variant
Location: chrX:2949459 (GRCh38)
Structure: AlphaFold pLDDT 92.57

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

Disease context

chondrodysplasia punctata, brachytelephalangic, autosomal — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

ARSL p.Ser233Leu Likely benign ★ same residue
ARSL c.24-2A>G Likely pathogenic ★★ same condition
ARSL p.Gly73Ser Likely pathogenic ★★ same condition
ARSL p.Ala182Thr Uncertain significance ★★ ⚠ same condition
ARSL p.Ala251Val Uncertain significance ★★ ⚠ same condition
ARSL p.Ala45Val Uncertain significance ★★ ⚠ same condition
ARSL p.Arg12Ser Uncertain significance ★★ ⚠ same condition
ARSL p.Arg190His 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/arsl-p-ser233 (accessed [today's date]).

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