Is AFF4 p.Glu657Asp (c.1971G>T) pathogenic?

AFF4 p.Glu657Asp (c.1971G>T) is classified Uncertain significance in AFF4 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-09-25). AlphaMissense: likely benign (0.0667); Absent from gnomAD v4.1; Associated with AFF4-related disorder.

How common is AFF4 p.Glu657Asp (c.1971G>T) in the general population?

AFF4 p.Glu657Asp (c.1971G>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about AFF4 p.Glu657Asp (c.1971G>T)?

AlphaMissense predicts likely benign (score 0.0667) — an in-silico prediction, not a clinical call.

AFF4 p.Glu657Asp

Q: What condition is associated with AFF4 p.Glu657Asp (c.1971G>T)?

AFF4 p.Glu657Asp (c.1971G>T) is associated with AFF4-related disorder, cognitive impairment - coarse facies - heart defects - obesity - pulmonary involvement - short stature - skeletal dysplasia syndrome (ClinVar).

c.1971G>T · rs760409554 · VCV2632048

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

AlphaMissense

likely benign

0.0667 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,613,914)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

AFF4-related disorder

Computational evidence

Protein change
AlphaMissense	0.0667	likely benign
REVEL	0.083	moderately benign-leaning
SaProt	LLR -6.08	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 4	GERP 4.6, phastCons 1
Regional constraint	o/e 0.84	unconstrained · MANE · 518 bp · p 0.026 · regional, not allelic
Overall
CADD	21.7	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

No allele count reported in gnomAD v4.1 (AN 1,613,914). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: AFF4
Protein: p.Glu657Asp
Coding: c.1971G>T
MANE Select: NM_014423
dbSNP: rs760409554
Type: single nucleotide variant
Location: chr5:132896659 (GRCh38)
Gene constraint: LOEUF 0.114 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 54.62 · 9 PDB
Residue 657: the 'disordered' region

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

Disease context

AFF4-related disorder

Also linked: cognitive impairment - coarse facies - heart defects - obesity - pulmonary involvement - short stature - skeletal dysplasia syndrome

Similar variants

AFF4 p.Arg258Trp Pathogenic/Likely pathogenic ★★ same condition
AFF4 p.Met260Val Likely pathogenic ★★ ⚠ same condition
AFF4 p.Pro253Leu Pathogenic/Likely pathogenic ★★ same condition
AFF4 p.Thr254Ser Pathogenic/Likely pathogenic ★★ ⚠ same condition
AFF4 c.1133+3A>G Uncertain significance ★★ same condition
AFF4 p.Ala114Thr Uncertain significance ★★ ⚠ same condition
AFF4 p.Ala114Val Uncertain significance ★★ ⚠ same condition
AFF4 p.Ala27Thr 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/aff4-p-glu657asp (accessed [today's date]).

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