Is RS1 p.Phe71= (c.213C>T) pathogenic?

RS1 p.Phe71= (c.213C>T) is classified Likely benign in RS1 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2023-12-01). Very rare (popmax 0.00296%, eas); Associated with X-linked retinoschisis.

What condition is associated with RS1 p.Phe71= (c.213C>T)?

RS1 p.Phe71= (c.213C>T) is associated with X-linked retinoschisis (ClinVar).

How common is RS1 p.Phe71= (c.213C>T) in the general population?

RS1 p.Phe71= (c.213C>T) is very rare (popmax 0.00296%, eas) (gnomAD).

RS1 p.Phe71=

c.213C>T · rs764292483 · VCV1126370

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00296%, eas)

Conditions

X-linked retinoschisis

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 -3.2	GERP -3.7
Overall
CADD	1.796	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00296% East Asian · 1/33,764 alleles

Filtering AF 0.000105% ClinGen BA1/BS1 input FAF95, joint · FAF99 7.1e-05%

Overall 0.000414% 5/1,208,869 alleles · very rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00296%	33,764
European (non-Finnish)	0.000447%	223,728

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.Phe71=
Coding: c.213C>T
MANE Select: NM_001323289 · reported on NM_000330
dbSNP: rs764292483
Type: single nucleotide variant
Location: chrX:18647304 (GRCh38)

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

Disease context

X-linked retinoschisis — 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/rs1-p-phe71 (accessed [today's date]).

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