Is RAB39B p.His110= (c.330C>T) pathogenic?

RAB39B p.His110= (c.330C>T) is classified Benign/Likely benign in RAB39B (ClinVar, Multiple submitters, 3 submitters; last evaluated 2021-10-12). Ultra-rare (popmax 0.0328%, amr); Associated with Inborn genetic diseases.

What condition is associated with RAB39B p.His110= (c.330C>T)?

RAB39B p.His110= (c.330C>T) is associated with Inborn genetic diseases (ClinVar).

How common is RAB39B p.His110= (c.330C>T) in the general population?

RAB39B p.His110= (c.330C>T) is ultra-rare (popmax 0.0328%, amr) (gnomAD).

RAB39B p.His110=

c.330C>T · rs782592713 · VCV1536817

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0328%, amr)

Conditions

Inborn genetic diseases

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 -0.53	GERP -3.7, phastCons 0.001
Overall
CADD	4.534	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0328% Admixed American · 15/45,791 alleles

Filtering AF 0.0202% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0163%

Overall 0.00141% 17/1,209,131 alleles · ultra-rare exomes 16/1,097,278 · genomes 1/111,853 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0328%	3,053
African / African-American	0.00175%	57,083
European (non-Finnish)	0.000112%	894,694

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: RAB39B
Protein: p.His110=
Coding: c.330C>T
MANE Select: NM_171998
dbSNP: rs782592713
Type: single nucleotide variant
Location: chrX:155261115 (GRCh38)
Structure: AlphaFold pLDDT 88.67 · 1 PDB

Full RAB39B gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

RAB39B p.Gly178Arg Uncertain significance ★★ ⚠ same condition
RAB39B p.Gly31= Benign/Likely benign ★★ same condition
RAB39B p.Gly42= Benign/Likely benign ★★ same condition
RAB39B p.Thr181= Benign/Likely benign ★★ same condition
RAB39B c.215+3G>A Conflicting classifications of pathogenicity ★ same condition
RAB39B p.Glu105Gly Uncertain significance ★ ⚠ same condition
RAB39B p.Glu184Gly Uncertain significance ★ ⚠ same condition
RAB39B p.Met147Val 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/rab39b-p-his110 (accessed [today's date]).

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