Is RAB7A p.Val29= (c.87G>A) pathogenic?

RAB7A p.Val29= (c.87G>A) is classified Benign/Likely benign in RAB7A (ClinVar, Multiple submitters, 10 submitters; last evaluated 2026-01-26). Rare (popmax 0.811%, eas); Associated with Inborn genetic diseases.

What condition is associated with RAB7A p.Val29= (c.87G>A)?

RAB7A p.Val29= (c.87G>A) is associated with Inborn genetic diseases, Charcot-Marie-Tooth disease type 2B, Charcot-Marie-Tooth disease (ClinVar).

How common is RAB7A p.Val29= (c.87G>A) in the general population?

RAB7A p.Val29= (c.87G>A) is rare (popmax 0.811%, eas) (gnomAD).

RAB7A p.Val29=

c.87G>A · rs145441548 · VCV343157

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 10 submitters

gnomAD v4.1

Rare

rare (popmax 0.811%, eas)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 6.4	phastCons 1
Overall
CADD	12.19	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.811% East Asian · 364/44,872 alleles

Filtering AF 0.743% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.716%

Overall 0.0402% 649/1,613,806 alleles · rare exomes 577/1,461,554 · genomes 72/152,252 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.811%	123
Ashkenazi Jewishnot grpmax-eligible	0.0878%	1,138
South Asian	0.0846%	1,183
Remaining individualsnot grpmax-eligible	0.056%	1,785
Middle Eastern	0.033%	3,031
European (non-Finnish)	0.0119%	8,427
Finnishnot grpmax-eligible	0.00469%	21,335
Admixed American	0.00333%	30,008

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: RAB7A
Protein: p.Val29=
Coding: c.87G>A
MANE Select: NM_004637
dbSNP: rs145441548
Type: single nucleotide variant
Location: chr3:128797976 (GRCh38)
Gene constraint: LOEUF 0.242 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 88.98 · 10 PDB
Residue 29: an α-helix

Full RAB7A 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

Also linked: Charcot-Marie-Tooth disease type 2B Charcot-Marie-Tooth disease

Similar variants

RAB7A p.Asn161Ile Pathogenic ★★ same condition
RAB7A p.Leu129Phe Pathogenic ★★ same condition
RAB7A p.Val162Met Pathogenic ★★ same condition
RAB7A c.*181G>A Uncertain significance ★★ same condition
RAB7A p.Arg69Gln Uncertain significance ★★ ⚠ same condition
RAB7A p.Ile169Thr Uncertain significance ★★ ⚠ same condition
RAB7A p.Leu56Pro Uncertain significance ★★ ⚠ same condition
RAB7A p.Ser155Asn 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/rab7a-p-val29 (accessed [today's date]).

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