Is IDE p.Ile978Val (c.2932A>G) pathogenic?

IDE p.Ile978Val (c.2932A>G) is classified Likely benign in IDE (ClinVar, Single submitter, 2 submitters; last evaluated 2021-12-02). AlphaMissense: likely benign (0.0563); Ultra-rare (popmax 0.0515%, nfe).

How common is IDE p.Ile978Val (c.2932A>G) in the general population?

IDE p.Ile978Val (c.2932A>G) is ultra-rare (popmax 0.0515%, nfe) (gnomAD).

What do computational predictors say about IDE p.Ile978Val (c.2932A>G)?

AlphaMissense predicts likely benign (score 0.0563) — an in-silico prediction, not a clinical call.

IDE p.Ile978Val

c.2932A>G · rs201349668 · VCV2355353

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.0563 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0515%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0563	likely benign
REVEL	0.017	moderately benign-leaning
SaProt	LLR -5.18	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 0.86	GERP -0.42, phastCons 0.82
Regional constraint	o/e 0.74	unconstrained · MANE · 56 kb · p 4.3e-15 · regional, not allelic
Overall
CADD	11.98	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0515% European (non-Finnish) · 603/1,171,010 alleles

Filtering AF 0.0481% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0467%

Overall 0.0387% 620/1,604,066 alleles · ultra-rare exomes 586/1,451,904 · genomes 34/152,162 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0515%	1,942
Remaining individualsnot grpmax-eligible	0.0129%	7,772
Finnishnot grpmax-eligible	0.00625%	16,003
African / African-American	0.00536%	18,674
South Asian	0.0011%	90,886

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: IDE
Protein: p.Ile978Val
Coding: c.2932A>G
MANE Select: NM_004969
dbSNP: rs201349668
Type: single nucleotide variant
Location: chr10:92455608 (GRCh38)
Gene constraint: LOEUF 0.638 · pLI 0.08 (gnomAD)
Structure: AlphaFold pLDDT 94.06 · 62 PDB

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

Similar variants

IDE p.Asn841= Benign ★★ same type
IDE p.His10= Benign/Likely benign ★★ same type
IDE p.Ile791= Benign ★★ same type
IDE p.Ala185Glu Uncertain significance ★ ⚠ same type
IDE p.Ala452Thr Uncertain significance ★ ⚠ same type
IDE p.Ala479Thr Uncertain significance ★ ⚠ same type
IDE p.Ala544Val Uncertain significance ★ ⚠ same type
IDE p.Ala610Val 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/ide-p-ile978val (accessed [today's date]).

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