Is ARL11 p.Ala68Thr (c.202G>A) pathogenic?

ARL11 p.Ala68Thr (c.202G>A) is classified Likely benign in ARL11 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-07-27). AlphaMissense: likely benign (0.0943); Absent from gnomAD v4.1.

How common is ARL11 p.Ala68Thr (c.202G>A) in the general population?

ARL11 p.Ala68Thr (c.202G>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about ARL11 p.Ala68Thr (c.202G>A)?

AlphaMissense predicts likely benign (score 0.0943) — an in-silico prediction, not a clinical call.

ARL11 p.Ala68Thr

c.202G>A · VCV3429929

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0943 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0943	likely benign
REVEL	0.236	benign-leaning
SaProt	LLR -8.11	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 0.24	GERP -4.7
Regional constraint	o/e 0.95	unconstrained · MANE · 587 bp · p 0.46 · regional, not allelic
Overall
CADD	0.053	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: ARL11
Protein: p.Ala68Thr
Coding: c.202G>A
MANE Select: NM_138450
Type: single nucleotide variant
Location: chr13:49630649 (GRCh38)
Gene constraint: LOEUF 1.844 · pLI 0.34 (gnomAD)
Structure: AlphaFold pLDDT 87.94

Full ARL11 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ARL11 p.Ala68Asp Uncertain significance ★ ⚠ same residue
ARL11 p.Trp149Ter Benign/Likely benign ★★ same type
ARL11 p.Ala129Val Uncertain significance ★ ⚠ same type
ARL11 p.Ala23Val Uncertain significance ★ ⚠ same type
ARL11 p.Arg138Gly Uncertain significance ★ ⚠ same type
ARL11 p.Arg176Cys Uncertain significance ★ ⚠ same type
ARL11 p.Arg190Cys Uncertain significance ★ ⚠ same type
ARL11 p.Arg95Cys 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/arl11-p-ala68thr (accessed [today's date]).

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