Is ANP32E p.Asp162Val (c.485A>T) pathogenic?

ANP32E p.Asp162Val (c.485A>T) is classified Uncertain significance in ANP32E (ClinVar, Single submitter, 1 submitter; last evaluated 2025-10-21). AlphaMissense: likely benign (0.1312); Very rare (popmax 8.48e-05%, nfe).

How common is ANP32E p.Asp162Val (c.485A>T) in the general population?

ANP32E p.Asp162Val (c.485A>T) is very rare (popmax 8.48e-05%, nfe) (gnomAD).

What do computational predictors say about ANP32E p.Asp162Val (c.485A>T)?

AlphaMissense predicts likely benign (score 0.1312) — an in-silico prediction, not a clinical call.

ANP32E p.Asp162Val

c.485A>T · VCV4641268

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1312 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 8.48e-05%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1312	likely benign
REVEL	0.131	moderately benign-leaning
SaProt	LLR -9.14	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	Δ0.22	donor gain · deltas
Constraint at this position
Conservation	phyloP 7.8	GERP 0.95, phastCons 1
Regional constraint	o/e 0.88	unconstrained · MANE · 8,416 bp · p 0.16 · regional, not allelic
Overall
CADD	24.7	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

Grpmax group 8.48e-05% European (non-Finnish) · 1/1,179,718 alleles

Overall 6.85e-05% 1/1,460,898 alleles · very rare

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: ANP32E
Protein: p.Asp162Val
Coding: c.485A>T
MANE Select: NM_030920
Type: single nucleotide variant
Location: chr1:150229080 (GRCh38)
Gene constraint: LOEUF 0.762 · pLI 0.06 (gnomAD)
Structure: AlphaFold pLDDT 76.34 · 2 PDB
Residue 162: the 'disordered' region

Full ANP32E gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ANP32E p.Asp162Glu Uncertain significance ★ ⚠ same residue
ANP32E p.Asp102Glu Uncertain significance ★ ⚠ same type
ANP32E p.Asp262Asn Uncertain significance ★ ⚠ same type
ANP32E p.Glu151Lys Uncertain significance ★ ⚠ same type
ANP32E p.Glu187Asp Uncertain significance ★ ⚠ same type
ANP32E p.Glu187Lys Uncertain significance ★ ⚠ same type
ANP32E p.Glu238Gly Uncertain significance ★ ⚠ same type
ANP32E p.Glu243Lys 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/anp32e-p-asp162val (accessed [today's date]).

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