Is ARSL p.Ala155Thr (c.463G>A) pathogenic?

ARSL p.Ala155Thr (c.463G>A) is classified Uncertain significance in ARSL (ClinVar, Single submitter, 1 submitter; last evaluated 2022-05-10). AlphaMissense: likely benign (0.072); Absent from gnomAD v4.1.

How common is ARSL p.Ala155Thr (c.463G>A) in the general population?

ARSL p.Ala155Thr (c.463G>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about ARSL p.Ala155Thr (c.463G>A)?

AlphaMissense predicts likely benign (score 0.072) — an in-silico prediction, not a clinical call.

ARSL p.Ala155Thr

c.463G>A · rs2518358997 · VCV1723854

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.072 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.072	likely benign
REVEL	0.253	benign-leaning
SaProt	LLR -4.73	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -5.6	GERP -3
Regional constraint	o/e 0.63	unconstrained · MANE · 26 kb · p 8.2e-17 · regional, not allelic
Overall
CADD	0.114	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

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.Ala155Thr
Coding: c.463G>A
MANE Select: NM_000047
dbSNP: rs2518358997
Type: single nucleotide variant
Location: chrX:2949695 (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-ala155thr (accessed [today's date]).

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