Is RIGI p.Asp772= (c.2316C>T) pathogenic?

RIGI p.Asp772= (c.2316C>T) is classified Likely benign in RIGI (ClinVar, Single submitter, 1 submitter; last evaluated 2025-06-09). Ultra-rare (popmax 0.0164%, mid).

How common is RIGI p.Asp772= (c.2316C>T) in the general population?

RIGI p.Asp772= (c.2316C>T) is ultra-rare (popmax 0.0164%, mid) (gnomAD).

RIGI p.Asp772=

c.2316C>T · rs372312705 · VCV1613341

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0164%, mid)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.6	GERP -3.9, phastCons 1
Overall
CADD	5.907	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0164% Middle Eastern · 1/6,082 alleles

Filtering AF 0.00157% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00134%

Overall 0.00211% 34/1,613,554 alleles · ultra-rare exomes 32/1,461,456 · genomes 2/152,098 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0164%	6,082
South Asian	0.0033%	30,346
Remaining individualsnot grpmax-eligible	0.0032%	31,232
European (non-Finnish)	0.00229%	43,698
East Asian	0.00223%	44,862

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.Asp772=
Coding: c.2316C>T
MANE Select: NM_014314
dbSNP: rs372312705
Type: single nucleotide variant
Location: chr9:32466311 (GRCh38)
Structure: AlphaFold pLDDT 85.40 · 44 PDB
Residue 772: the helicase c-terminal domain; the 'interaction with zc3hav1' region; the 'mediates interaction with rnf135' region

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

Similar variants

RIGI p.Asp772Glu Uncertain significance ★ ⚠ same residue
RIGI c.1923+1G>A Uncertain significance ★★ same type
RIGI c.954-6T>G Uncertain significance ★★ same type
RIGI p.Ala436Val Uncertain significance ★★ ⚠ same type
RIGI p.Ala486Thr Uncertain significance ★★ ⚠ same type
RIGI p.Ala537Ser Uncertain significance ★★ ⚠ same type
RIGI p.Ala537Thr Uncertain significance ★★ ⚠ same type
RIGI p.Ala774Thr 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-asp772 (accessed [today's date]).

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