Is RIGI p.Val800= (c.2400A>C) pathogenic?

RIGI p.Val800= (c.2400A>C) is classified Benign/Likely benign in RIGI (ClinVar, Multiple submitters, 5 submitters; last evaluated 2026-02-04). Common (popmax 44.4%, eas) — too common for a highly-penetrant pathogenic allele; Associated with Singleton-Merten syndrome 2.

What condition is associated with RIGI p.Val800= (c.2400A>C)?

RIGI p.Val800= (c.2400A>C) is associated with Singleton-Merten syndrome 2 (ClinVar).

RIGI p.Val800=

Q: How common is RIGI p.Val800= (c.2400A>C) in the general population?

RIGI p.Val800= (c.2400A>C) is common (popmax 44.4%, eas) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.2400A>C · rs3205166 · VCV1169347

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 5 submitters

gnomAD v4.1

Common

common (popmax 44.4%, eas) — too common for a highly-penetrant pathogenic allele

Conditions

Singleton-Merten syndrome 2

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -0.53	GERP -3
Overall
CADD	3.803	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 44.4% East Asian · 19,902/44,818 alleles

Filtering AF 43.9% ClinGen BA1/BS1 input FAF95, joint · FAF99 43.7%

Overall 34.7% 559,800/1,612,956 alleles · common exomes 510,361/1,460,910 · genomes 49,439/152,046 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	44.4%	2
Ashkenazi Jewishnot grpmax-eligible	39.7%	3
Middle Eastern	38.5%	3
European (non-Finnish)	35.7%	3
Remaining individualsnot grpmax-eligible	35%	3
Amishnot grpmax-eligible	34.8%	3
Admixed American	34.5%	3
Finnishnot grpmax-eligible	32.8%	3
South Asian	25.4%	4
African / African-American	23.3%	4

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.Val800=
Coding: c.2400A>C
MANE Select: NM_014314
dbSNP: rs3205166
Type: single nucleotide variant
Location: chr9:32459452 (GRCh38)

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

Disease context

Singleton-Merten syndrome 2 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

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-val800 (accessed [today's date]).

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