Is RIGI p.Phe310fs (c.929del) pathogenic?

RIGI p.Phe310fs (c.929del) is classified Likely benign in RIGI (ClinVar, Single submitter, 1 submitter; last evaluated 2026-01-12). Rare (popmax 0.154%, sas).

How common is RIGI p.Phe310fs (c.929del) in the general population?

RIGI p.Phe310fs (c.929del) is rare (popmax 0.154%, sas) (gnomAD).

RIGI p.Phe310fs

c.929del · rs756983208 · VCV1593083

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

rare (popmax 0.154%, sas)

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 7 of 18
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 4	GERP -2.7, phastCons 1
Overall
CADD	32.0	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.154% South Asian · 138/89,874 alleles

Filtering AF 0.133% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.125%

Overall 0.00913% 147/1,609,416 alleles · rare exomes 144/1,457,138 · genomes 3/152,278 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.154%	651
Remaining individualsnot grpmax-eligible	0.0145%	6,919

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: RIGI
Protein: p.Phe310fs
Coding: c.929del
MANE Select: NM_014314
dbSNP: rs756983208
Type: Deletion
Location: chr9:32488758 (GRCh38)
Structure: AlphaFold pLDDT 85.40 · 44 PDB
Residue 310: the helicase atp-binding domain; the 'interaction with zc3hav1' region; an α-helix

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

Similar variants

RIGI c.106+4_106+5del Benign/Likely benign ★★ same type
RIGI c.1376-12del Benign/Likely benign ★★ same type
RIGI c.1481-6del Benign/Likely benign ★★ same type
RIGI c.242-4del Benign/Likely benign ★★ same type
RIGI c.954-21_954-20del Benign/Likely benign ★★ same type
RIGI c.688_691+6del Uncertain significance ★ same type
RIGI p.Ala642_Leu643insTer Uncertain significance ★ same type
RIGI p.Arg734fs Uncertain significance ★ 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/rigi-p-phe310fs (accessed [today's date]).

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