Is APOBR p.Arg5Trp (c.13C>T) pathogenic?

APOBR p.Arg5Trp (c.13C>T) is classified Uncertain significance in APOBR (ClinVar, Single submitter, 1 submitter; last evaluated 2024-04-09). AlphaMissense: likely benign (0.3143); Ultra-rare (popmax 0.0268%, amr).

How common is APOBR p.Arg5Trp (c.13C>T) in the general population?

APOBR p.Arg5Trp (c.13C>T) is ultra-rare (popmax 0.0268%, amr) (gnomAD).

What do computational predictors say about APOBR p.Arg5Trp (c.13C>T)?

AlphaMissense predicts likely benign (score 0.3143) — an in-silico prediction, not a clinical call.

APOBR p.Arg5Trp

c.13C>T · VCV3308383

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.3143 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0268%, amr)

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.3143	likely benign · top 7% in APOBR
REVEL	0.475	indeterminate
SaProt	LLR -11.43	damaging
⇒ SaProt calls this damaging; AlphaMissense does not; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4.8	GERP 1.7, phastCons 1
Regional constraint	o/e 1.03	unconstrained · MANE · 3,820 bp · p 0.27 · regional, not allelic
Overall
CADD	28.8	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

Grpmax group 0.0268% Admixed American · 16/59,790 alleles

Filtering AF 0.0168% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0137%

Overall 0.00223% 36/1,612,226 alleles · ultra-rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0268%	3,737
South Asian	0.0044%	22,726
Finnishnot grpmax-eligible	0.00156%	63,972
European (non-Finnish)	0.00127%	78,597

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: APOBR
Protein: p.Arg5Trp
Coding: c.13C>T
MANE Select: NM_018690
Type: single nucleotide variant
Location: chr16:28494694 (GRCh38)
Gene constraint: LOEUF 0.99 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 41.14

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

Similar variants

APOBR p.Gln807Pro Benign ★★ same type
APOBR p.Gly350= Likely benign ★★ same type
APOBR p.Ala241Gly Uncertain significance ★ ⚠ same type
APOBR p.Ala283Val Uncertain significance ★ ⚠ same type
APOBR p.Ala292Val Uncertain significance ★ ⚠ same type
APOBR p.Ala301Thr Uncertain significance ★ ⚠ same type
APOBR p.Ala33Val Uncertain significance ★ ⚠ same type
APOBR p.Ala514Asp 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/apobr-p-arg5trp (accessed [today's date]).

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