Is ARL2BP p.Phe13= (c.39C>T) pathogenic?

ARL2BP p.Phe13= (c.39C>T) is classified Likely benign in ARL2BP (ClinVar, Single submitter, 1 submitter; last evaluated 2025-11-24). Very rare (popmax 0.00134%, afr); Associated with Inborn genetic diseases.

What condition is associated with ARL2BP p.Phe13= (c.39C>T)?

ARL2BP p.Phe13= (c.39C>T) is associated with Inborn genetic diseases (ClinVar).

How common is ARL2BP p.Phe13= (c.39C>T) in the general population?

ARL2BP p.Phe13= (c.39C>T) is very rare (popmax 0.00134%, afr) (gnomAD).

ARL2BP p.Phe13=

c.39C>T · VCV4585172

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00134%, afr)

Conditions

Inborn genetic diseases

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 1.3	GERP -0.039, phastCons 1
Overall
CADD	17.59	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00134% African / African-American · 1/74,886 alleles

Overall 6.2e-05% 1/1,613,834 alleles · very rare exomes 0/1,461,700 · genomes 1/152,134 · joint denominator

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: ARL2BP
Protein: p.Phe13=
Coding: c.39C>T
MANE Select: NM_012106
Type: single nucleotide variant
Location: chr16:57246080 (GRCh38)
Gene constraint: LOEUF 1.03 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 82.01 · 3 PDB

Full ARL2BP gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

ARL2BP p.Ala16Ser Uncertain significance ★★ ⚠ same condition
ARL2BP p.Arg84Gln Uncertain significance ★★ ⚠ same condition
ARL2BP p.Arg84Trp Uncertain significance ★★ same condition
ARL2BP p.Asn159Lys Uncertain significance ★★ ⚠ same condition
ARL2BP p.Asp110Asn Uncertain significance ★★ ⚠ same condition
ARL2BP p.Asp22Val Uncertain significance ★★ ⚠ same condition
ARL2BP p.Glu36Lys Uncertain significance ★★ ⚠ same condition
ARL2BP p.Gly136Arg 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/arl2bp-p-phe13 (accessed [today's date]).

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