Is AFF4 p.Asp60Glu (c.180T>A) pathogenic?

AFF4 p.Asp60Glu (c.180T>A) is classified Uncertain significance in AFF4 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-01-31). AlphaMissense: likely benign (0.3127); Absent from gnomAD v4.1.

How common is AFF4 p.Asp60Glu (c.180T>A) in the general population?

AFF4 p.Asp60Glu (c.180T>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about AFF4 p.Asp60Glu (c.180T>A)?

AlphaMissense predicts likely benign (score 0.3127) — an in-silico prediction, not a clinical call.

AFF4 p.Asp60Glu

c.180T>A · VCV4072682

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.3127 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.3127	likely benign
REVEL	0.22	benign-leaning
SaProt	LLR -8.19	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 6.7	GERP 2.9, phastCons 1
Regional constraint	o/e 0.49	unconstrained · MANE · 2,298 bp · p 2e-05 · regional, not allelic
Overall
CADD	23.8	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

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: AFF4
Protein: p.Asp60Glu
Coding: c.180T>A
MANE Select: NM_014423
Type: single nucleotide variant
Location: chr5:132934885 (GRCh38)
Gene constraint: LOEUF 0.114 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 54.62 · 9 PDB
Residue 60: an α-helix

Full AFF4 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

AFF4 p.Asp60Asn Uncertain significance ★★ ⚠ same residue
AFF4 p.Asp60= Likely benign ★ same residue
AFF4 p.Arg258Trp Pathogenic/Likely pathogenic ★★ same type
AFF4 p.Met260Val Likely pathogenic ★★ ⚠ same type
AFF4 p.Pro253Leu Pathogenic/Likely pathogenic ★★ same type
AFF4 p.Thr254Ser Pathogenic/Likely pathogenic ★★ ⚠ same type
AFF4 c.1133+3A>G Uncertain significance ★★ same type
AFF4 p.Ala114Thr 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/aff4-p-asp60glu (accessed [today's date]).

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