Is RANBP2 p.Arg840= (c.2520T>C) pathogenic?

RANBP2 p.Arg840= (c.2520T>C) is classified Benign/Likely benign in RANBP2 (ClinVar, Multiple submitters, 4 submitters; last evaluated 2025-01-06). Rare (popmax 0.186%, nfe); Associated with familial acute necrotizing encephalopathy.

What condition is associated with RANBP2 p.Arg840= (c.2520T>C)?

RANBP2 p.Arg840= (c.2520T>C) is associated with familial acute necrotizing encephalopathy (ClinVar).

How common is RANBP2 p.Arg840= (c.2520T>C) in the general population?

RANBP2 p.Arg840= (c.2520T>C) is rare (popmax 0.186%, nfe) (gnomAD).

How is Familial acute necrotizing encephalopathy inherited?

Typically Autosomal dominant (Orphanet). A genetic counselor can assess individual risk for a family.

RANBP2 p.Arg840=

c.2520T>C · rs150539591 · VCV384587

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

rare (popmax 0.186%, nfe)

Conditions

familial acute necrotizing encephalopathy

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.16	GERP -3.1, phastCons 0.67
Overall
CADD	7.229	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.186% European (non-Finnish) · 2,191/1,179,850 alleles

Filtering AF 0.179% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.177%

Overall 0.144% 2,322/1,611,846 alleles · rare exomes 2,220/1,459,708 · genomes 102/152,138 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.186%	538
Remaining individualsnot grpmax-eligible	0.141%	708
African / African-American	0.0454%	2,202
Admixed American	0.00834%	11,996
Finnishnot grpmax-eligible	0.00625%	16,008

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: RANBP2
Protein: p.Arg840=
Coding: c.2520T>C
MANE Select: NM_006267
dbSNP: rs150539591
Type: single nucleotide variant
Location: chr2:108758466 (GRCh38)
Gene constraint: LOEUF 0.231 · pLI 1.00 (gnomAD)

Full RANBP2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

familial acute necrotizing encephalopathy — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Familial acute necrotizing encephalopathy (Orphanet):

Inheritance: Autosomal dominant
Onset: Adolescent, Adult, Childhood, Infancy

Similar variants

RANBP2 p.Thr585Met Pathogenic/Likely pathogenic ★★ ⚠ same condition
RANBP2 c.406-2A>G Uncertain significance ★★ same condition
RANBP2 p.Ala2564Ser Uncertain significance ★★ ⚠ same condition
RANBP2 p.Ala3072Val Uncertain significance ★★ ⚠ same condition
RANBP2 p.Ala534Val Uncertain significance ★★ same condition
RANBP2 p.Ala836Val Uncertain significance ★★ ⚠ same condition
RANBP2 p.Arg1096Gln Uncertain significance ★★ ⚠ same condition
RANBP2 p.Arg1198Cys 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/ranbp2-p-arg840 (accessed [today's date]).

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