Is RAG1 p.Arg930Met (c.2789G>T) pathogenic?

RAG1 p.Arg930Met (c.2789G>T) is classified Uncertain significance in RAG1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-12-29). AlphaMissense: likely pathogenic (0.9676); Very rare (popmax 0.0011%, sas); Associated with Inborn genetic diseases.

What condition is associated with RAG1 p.Arg930Met (c.2789G>T)?

RAG1 p.Arg930Met (c.2789G>T) is associated with Inborn genetic diseases (ClinVar).

How common is RAG1 p.Arg930Met (c.2789G>T) in the general population?

RAG1 p.Arg930Met (c.2789G>T) is very rare (popmax 0.0011%, sas) (gnomAD).

What do computational predictors say about RAG1 p.Arg930Met (c.2789G>T)?

AlphaMissense predicts likely pathogenic (score 0.9676) — an in-silico prediction, not a clinical call.

RAG1 p.Arg930Met

c.2789G>T · VCV4838657

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9676 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.0011%, sas)

Missense predictors

2/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.9676	likely pathogenic
REVEL	0.749	pathogenic-leaning
SaProt	LLR -6.96	tolerated
⇒ AlphaMissense and REVEL call this damaging; SaProt does not.
Splicing
SpliceAI	Δ0.70	donor loss at this position · masked 0 · deltas
Constraint at this position
Conservation	phyloP 12	GERP 2.8, phastCons 1
Regional constraint	o/e 0.85	unconstrained · MANE · 2,313 bp · p 3.1e-06 · regional, not allelic
Overall
CADD	32.0	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0011% South Asian · 1/91,072 alleles

Overall 6.84e-05% 1/1,461,726 alleles · very rare

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: RAG1
Protein: p.Arg930Met
Coding: c.2789G>T
MANE Select: NM_000448
Type: single nucleotide variant
Location: chr11:36576093 (GRCh38)
Gene constraint: LOEUF 0.703 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 81.68
Residue 930: a UniProt-annotated variant site (in t(-)b(-)nk(+) scid; uncertain significance); a UniProt-annotated variant site (in t(-)b(-)nk(+) scid; uncertain significance; also found in patients with an atypical form of severe combined immunodeficiency/omenn syndrome; uncertain significance; loss of recombination activity)

Full RAG1 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

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RAG1 p.Glu95Lys Uncertain significance ★★ ⚠ same condition
RAG1 p.His636Arg Uncertain significance ★★ ⚠ same condition
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RAG1 p.Ile815Met 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/rag1-p-arg930met (accessed [today's date]).

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