Is RAB3GAP2 p.Asp13= (c.39C>T) pathogenic?

RAB3GAP2 p.Asp13= (c.39C>T) is classified Benign/Likely benign in RAB3GAP2 (ClinVar, Multiple submitters, 7 submitters; last evaluated 2025-12-21). Rare (popmax 0.491%, afr); Associated with Warburg micro syndrome 2.

What condition is associated with RAB3GAP2 p.Asp13= (c.39C>T)?

RAB3GAP2 p.Asp13= (c.39C>T) is associated with Warburg micro syndrome 2, Martsolf syndrome (ClinVar).

How common is RAB3GAP2 p.Asp13= (c.39C>T) in the general population?

RAB3GAP2 p.Asp13= (c.39C>T) is rare (popmax 0.491%, afr) (gnomAD).

RAB3GAP2 p.Asp13=

c.39C>T · rs145667920 · VCV295673

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 7 submitters

gnomAD v4.1

Rare

rare (popmax 0.491%, afr)

Conditions

Warburg micro syndrome 2

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 4.8	GERP 0.93, phastCons 1
Overall
CADD	13.47	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.491% African / African-American · 368/74,976 alleles

Filtering AF 0.449% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.433%

Overall 0.0243% 392/1,612,502 alleles · rare exomes 188/1,460,526 · genomes 204/151,976 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.491%	204
Remaining individualsnot grpmax-eligible	0.024%	4,165
Admixed American	0.0117%	8,559
European (non-Finnish)	0.00017%	589,824

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: RAB3GAP2
Protein: p.Asp13=
Coding: c.39C>T
MANE Select: NM_012414
dbSNP: rs145667920
Type: single nucleotide variant
Location: chr1:220272299 (GRCh38)
Gene constraint: LOEUF 0.535 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 79.77 · 1 PDB

Full RAB3GAP2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Warburg micro syndrome 2 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: Martsolf syndrome

Similar variants

RAB3GAP2 c.713-2A>C Likely pathogenic ★★ same condition
RAB3GAP2 p.Arg1213Ter Pathogenic ★★ same condition
RAB3GAP2 p.Arg426Cys Pathogenic/Likely pathogenic ★★ same condition
RAB3GAP2 c.*2171A>G Uncertain significance ★★ same condition
RAB3GAP2 p.Ala16Thr Uncertain significance ★★ ⚠ same condition
RAB3GAP2 p.Ala240Pro Uncertain significance ★★ ⚠ same condition
RAB3GAP2 p.Ala300Thr Uncertain significance ★★ ⚠ same condition
RAB3GAP2 p.Ala684Glu 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/rab3gap2-p-asp13 (accessed [today's date]).

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