Is RS1 p.Arg102= (c.306G>T) pathogenic?

RS1 p.Arg102= (c.306G>T) is classified Likely benign in RS1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-04-03). Ultra-rare (popmax 0.0123%, sas).

How common is RS1 p.Arg102= (c.306G>T) in the general population?

RS1 p.Arg102= (c.306G>T) is ultra-rare (popmax 0.0123%, sas) (gnomAD).

RS1 p.Arg102=

c.306G>T · rs762601581 · VCV1102298

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0123%, sas)

⚠ 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 -0.45	GERP -1.1, phastCons 0.032
Overall
CADD	5.761	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0123% South Asian · 7/56,698 alleles

Filtering AF 0.00571% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00408%

Overall 0.000662% 8/1,208,782 alleles · ultra-rare exomes 7/1,097,948 · genomes 1/110,834 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0123%	8,100
Remaining individualsnot grpmax-eligible	0.0021%	47,548

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: RS1
Protein: p.Arg102=
Coding: c.306G>T
MANE Select: NM_000330
dbSNP: rs762601581
Type: single nucleotide variant
Location: chrX:18647211 (GRCh38)

Full RS1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

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/rs1-p-arg102 (accessed [today's date]).

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