Is ASB15 p.Phe458Ser (c.1373T>C) pathogenic?

ASB15 p.Phe458Ser (c.1373T>C) is classified Uncertain significance in ASB15 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-02-27). AlphaMissense: likely benign (0.2845); Ultra-rare (popmax 0.052%, afr).

How common is ASB15 p.Phe458Ser (c.1373T>C) in the general population?

ASB15 p.Phe458Ser (c.1373T>C) is ultra-rare (popmax 0.052%, afr) (gnomAD).

What do computational predictors say about ASB15 p.Phe458Ser (c.1373T>C)?

AlphaMissense predicts likely benign (score 0.2845) — an in-silico prediction, not a clinical call.

ASB15 p.Phe458Ser

c.1373T>C · rs144320147 · VCV3130126

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2845 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.052%, afr)

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.2845	likely benign
REVEL	0.313	indeterminate
SaProt	LLR -5.13	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 6.2	GERP 2.2, phastCons 1
Regional constraint	o/e 0.96	unconstrained · MANE · 22 kb · p 0.3 · regional, not allelic
Overall
CADD	20.3	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

Grpmax group 0.052% African / African-American · 39/75,004 alleles

Filtering AF 0.039% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0345%

Overall 0.00279% 45/1,613,976 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.052%	1,923
Admixed American	0.00333%	30,006
Remaining individualsnot grpmax-eligible	0.0032%	31,254
European (non-Finnish)	0.000169%	589,995

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: ASB15
Protein: p.Phe458Ser
Coding: c.1373T>C
MANE Select: NM_001290258
dbSNP: rs144320147
Type: single nucleotide variant
Location: chr7:123629367 (GRCh38)
Gene constraint: LOEUF 1.186 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 87.39

Full ASB15 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ASB15 p.Phe458Leu Uncertain significance ★ ⚠ same residue
ASB15 p.Ala194Thr Uncertain significance ★ ⚠ same type
ASB15 p.Ala250Thr Uncertain significance ★ ⚠ same type
ASB15 p.Ala315Gly Uncertain significance ★ ⚠ same type
ASB15 p.Ala372Thr Uncertain significance ★ ⚠ same type
ASB15 p.Ala558Val Uncertain significance ★ ⚠ same type
ASB15 p.Ala568Pro Uncertain significance ★ ⚠ same type
ASB15 p.Ala72Ser 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/asb15-p-phe458ser (accessed [today's date]).

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