Is RABL6 p.Pro486Ser (c.1456C>T) pathogenic?

RABL6 p.Pro486Ser (c.1456C>T) is classified Uncertain significance in RABL6 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-02-28). AlphaMissense: likely benign (0.0704); Rare (popmax 0.187%, mid).

How common is RABL6 p.Pro486Ser (c.1456C>T) in the general population?

RABL6 p.Pro486Ser (c.1456C>T) is rare (popmax 0.187%, mid) (gnomAD).

What do computational predictors say about RABL6 p.Pro486Ser (c.1456C>T)?

AlphaMissense predicts likely benign (score 0.0704) — an in-silico prediction, not a clinical call.

RABL6 p.Pro486Ser

c.1456C>T · rs753215354 · VCV3150952

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0704 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.187%, mid)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0704	likely benign
REVEL	0.115	moderately benign-leaning
SaProt	LLR -7.53	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 0.58	GERP -0.073
Regional constraint	o/e 1.26	unconstrained · MANE · 2,621 bp · p 1.7e-08 · regional, not allelic
Overall
CADD	6.18	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.187% Middle Eastern · 11/5,876 alleles

Filtering AF 0.105% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0812%

Overall 0.00254% 41/1,612,260 alleles · rare exomes 40/1,460,076 · genomes 1/152,184 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.187%	534
Remaining individualsnot grpmax-eligible	0.00961%	10,401
South Asian	0.0022%	45,534
European (non-Finnish)	0.00178%	56,181
Admixed American	0.00167%	59,980

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: RABL6
Protein: p.Pro486Ser
Coding: c.1456C>T
MANE Select: NM_024718
dbSNP: rs753215354
Type: single nucleotide variant
Location: chr9:136839084 (GRCh38)
Gene constraint: LOEUF 0.588 · pLI 0.15 (gnomAD)
Structure: AlphaFold pLDDT 60.84
Residue 486: the 'disordered' region

Full RABL6 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

RABL6 p.Pro486Leu Likely benign ★ same residue
RABL6 p.Arg690Gln Uncertain significance ★★ ⚠ same type
RABL6 p.Ser402Thr Uncertain significance ★★ ⚠ same type
RABL6 p.Ser535Gly Uncertain significance ★★ ⚠ same type
RABL6 p.Arg280His Benign/Likely benign ★★ same type
RABL6 p.Arg533His Benign ★★ same type
RABL6 p.Pro518Leu Benign ★★ same type
RABL6 p.Pro539= Benign ★★ 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/rabl6-p-pro486ser (accessed [today's date]).

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