Is ARSL p.Arg285Lys (c.854G>A) pathogenic?

ARSL p.Arg285Lys (c.854G>A) is classified Likely pathogenic in ARSL (ClinVar, Single submitter, 1 submitter; last evaluated 2025-05-15). AlphaMissense: likely benign (0.1061); Absent from gnomAD v4.1.

How common is ARSL p.Arg285Lys (c.854G>A) in the general population?

ARSL p.Arg285Lys (c.854G>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about ARSL p.Arg285Lys (c.854G>A)?

AlphaMissense predicts likely benign (score 0.1061) — an in-silico prediction, not a clinical call.

ARSL p.Arg285Lys

c.854G>A · rs2147378714 · VCV1200861

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1061 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.1061	likely benign ⚠ discordant with ClinVar
REVEL	0.316	indeterminate
SaProt	LLR -6.29	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL makes no call.
Splicing
SpliceAI	Δ0.65	donor loss · deltas
Pangolin	Δ0.41	loss · gain 0.05 · agrees with SpliceAI · independent
Constraint at this position
Conservation	phyloP 2.1	GERP 1.3, phastCons 0.98
Regional constraint	o/e 0.63	unconstrained · MANE · 26 kb · p 8.2e-17 · regional, not allelic
Overall
CADD	24.2	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: ARSL
Protein: p.Arg285Lys
Coding: c.854G>A
MANE Select: NM_000047
dbSNP: rs2147378714
Type: single nucleotide variant
Location: chrX:2949304 (GRCh38)
Structure: AlphaFold pLDDT 92.57

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

Similar variants

ARSL c.1289+1G>A Pathogenic/Likely pathogenic ★★ same type
ARSL c.24-2A>G Likely pathogenic ★★ same type
ARSL p.Arg111Cys Likely pathogenic ★★ same type
ARSL p.Gly117Arg Pathogenic/Likely pathogenic ★★ same type
ARSL p.Gly73Ser Likely pathogenic ★★ ⚠ same type
ARSL p.Ala182Thr Uncertain significance ★★ ⚠ same type
ARSL p.Ala251Val Uncertain significance ★★ ⚠ same type
ARSL p.Ala45Val Uncertain significance ★★ ⚠ same type

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-arg285lys (accessed [today's date]).

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