Is RD3 p.Ala50Val (c.149C>T) pathogenic?

RD3 p.Ala50Val (c.149C>T) is classified Uncertain significance in RD3 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-07-29). AlphaMissense: likely benign (0.0859); Ultra-rare (popmax 0.0133%, amr); Associated with Leber congenital amaurosis 12.

What condition is associated with RD3 p.Ala50Val (c.149C>T)?

RD3 p.Ala50Val (c.149C>T) is associated with Leber congenital amaurosis 12 (ClinVar).

How common is RD3 p.Ala50Val (c.149C>T) in the general population?

RD3 p.Ala50Val (c.149C>T) is ultra-rare (popmax 0.0133%, amr) (gnomAD).

How is Leber congenital amaurosis inherited?

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

What do computational predictors say about RD3 p.Ala50Val (c.149C>T)?

AlphaMissense predicts likely benign (score 0.0859) — an in-silico prediction, not a clinical call.

RD3 p.Ala50Val

c.149C>T · rs140156866 · VCV2199823

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0859 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0133%, amr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Leber congenital amaurosis 12

Computational evidence

Protein change
AlphaMissense	0.0859	likely benign
REVEL	0.054	moderately benign-leaning
SaProt	LLR -7.34	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 1.1	GERP -1.4
Regional constraint	o/e 1.02	unconstrained · MANE · 2,376 bp · p 0.68 · regional, not allelic
Overall
CADD	15.91	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 0.0133% Admixed American · 8/60,012 alleles

Filtering AF 0.00661% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00482%

Overall 0.00273% 44/1,614,146 alleles · ultra-rare exomes 34/1,461,874 · genomes 10/152,272 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0133%	7,501
African / African-American	0.012%	8,328
Remaining individualsnot grpmax-eligible	0.008%	12,498
East Asian	0.00445%	22,451
European (non-Finnish)	0.00169%	59,003

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: RD3
Protein: p.Ala50Val
Coding: c.149C>T
MANE Select: NM_001164688
dbSNP: rs140156866
Type: single nucleotide variant
Location: chr1:211481267 (GRCh38)
Gene constraint: LOEUF 1.116 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 80.99 · 1 PDB
Residue 50: an α-helix

Full RD3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Leber congenital amaurosis 12 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Leber congenital amaurosis (Orphanet):

Inheritance: Autosomal dominant, Autosomal recessive
Onset: Infancy, Neonatal
Prevalence: 1-9 / 100 000 (Europe)

Similar variants

RD3 p.Ala50= Conflicting classifications of pathogenicity ★ same residue
RD3 p.Ala50Glu Uncertain significance ★ ⚠ same residue
RD3 p.Ala50Thr Uncertain significance ★ ⚠ same residue
RD3 c.296+1G>T Pathogenic/Likely pathogenic ★★ same condition
RD3 p.Arg38Ter Pathogenic ★★ same condition
RD3 p.Tyr60Ter Pathogenic ★★ same condition
RD3 c.-572G>A Uncertain significance ★★ same condition
RD3 c.*1277G>A 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/rd3-p-ala50val (accessed [today's date]).

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