Is ASB1 p.Arg153= (c.459C>T) pathogenic?

ASB1 p.Arg153= (c.459C>T) is classified Likely benign in ASB1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-12-09). Very rare (popmax 0.00288%, nfe).

How common is ASB1 p.Arg153= (c.459C>T) in the general population?

ASB1 p.Arg153= (c.459C>T) is very rare (popmax 0.00288%, nfe) (gnomAD).

ASB1 p.Arg153=

c.459C>T · VCV4643319

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00288%, nfe)

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 -15	GERP -3.2
Overall
CADD	0.123	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00288% European (non-Finnish) · 34/1,179,916 alleles

Filtering AF 0.00207% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00183%

Overall 0.00229% 37/1,613,510 alleles · very rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00288%	34,703
East Asian	0.00223%	44,892
Admixed American	0.00167%	59,988
Remaining individualsnot grpmax-eligible	0.0016%	62,480

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: ASB1
Protein: p.Arg153=
Coding: c.459C>T
MANE Select: NM_001040445
Type: single nucleotide variant
Location: chr2:238435978 (GRCh38)
Gene constraint: LOEUF 0.951 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 80.61

Full ASB1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ASB1 p.Ala11Gly Uncertain significance ★ ⚠ same type
ASB1 p.Ala216Val Uncertain significance ★ ⚠ same type
ASB1 p.Ala85Val Uncertain significance ★ ⚠ same type
ASB1 p.Arg141Trp Uncertain significance ★ ⚠ same type
ASB1 p.Arg144Cys Uncertain significance ★ ⚠ same type
ASB1 p.Arg144His Uncertain significance ★ ⚠ same type
ASB1 p.Arg156Gln Uncertain significance ★ ⚠ same type
ASB1 p.Arg165Ser 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/asb1-p-arg153 (accessed [today's date]).

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