Is RASGRP1 p.Arg439fs (c.1307_1314dup) pathogenic?

RASGRP1 p.Arg439fs (c.13071314dup) is classified Pathogenic in RASGRP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-08-08). No gnomAD frequency available for this variant.

How common is RASGRP1 p.Arg439fs (c.1307_1314dup) in the general population?

RASGRP1 p.Arg439fs (c.1307_1314dup) is no gnomAD frequency available for this variant (gnomAD).

RASGRP1 p.Arg439fs

c.1307_1314dup · rs2542878863 · VCV2022859

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 10 of 17
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 2.9	GERP 2.4, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: RASGRP1
Protein: p.Arg439fs
Coding: c.1307_1314dup
MANE Select: NM_005739
dbSNP: rs2542878863
Type: Duplication
Location: chr15:38505848 (GRCh38)
Gene constraint: LOEUF 0.538 · pLI 0.48 (gnomAD)
Structure: AlphaFold pLDDT 72.43 · 2 PDB
Residue 439: a UniProt-annotated variant site (in imd64; loss of protein expression); a UniProt-annotated variant site (in imd64); a UniProt-annotated variant site (in imd64; no effect on protein expression; decreased t cell activation)

Full RASGRP1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

RASGRP1 p.Ala638fs Pathogenic ★ same type
RASGRP1 p.Asp74Ter Pathogenic ★ same type
RASGRP1 p.Val316fs Pathogenic ★ same type
RASGRP1 c.1874-6dup Likely benign ★ same type
RASGRP1 c.390-17dup Benign ★ same type
RASGRP1 c.390-20_390-17dup Likely benign ★ same type
RASGRP1 c.850-100dup 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/rasgrp1-p-arg439fs (accessed [today's date]).

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