Is RGR p.Ser106= (c.318T>C) pathogenic?

RGR p.Ser106= (c.318T>C) is classified Conflicting classifications of pathogenicity in RGR (ClinVar, Conflicting submitters, 6 submitters; last evaluated 2026-01-27). Rare (popmax 0.15%, nfe); Associated with retinitis pigmentosa.

What condition is associated with RGR p.Ser106= (c.318T>C)?

RGR p.Ser106= (c.318T>C) is associated with retinitis pigmentosa (ClinVar).

How common is RGR p.Ser106= (c.318T>C) in the general population?

RGR p.Ser106= (c.318T>C) is rare (popmax 0.15%, nfe) (gnomAD).

How is Retinitis pigmentosa inherited?

Typically Autosomal dominant, Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

RGR p.Ser106=

c.318T>C · rs143761967 · VCV167591

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 6 submitters

gnomAD v4.1

Rare

rare (popmax 0.15%, nfe)

Conditions

retinitis pigmentosa

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.075	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -5.3	GERP 1.3
Overall
CADD	7.29	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.15% European (non-Finnish) · 1,773/1,179,968 alleles

Filtering AF 0.144% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.142%

Overall 0.122% 1,976/1,613,944 alleles · rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.15%	666
Remaining individualsnot grpmax-eligible	0.131%	762
Admixed American	0.122%	822
African / African-American	0.032%	3,121
Finnishnot grpmax-eligible	0.0265%	3,767
Ashkenazi Jewishnot grpmax-eligible	0.0101%	9,869
East Asian	0.00891%	11,220

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: RGR
Protein: p.Ser106=
Coding: c.318T>C
MANE Select: NM_153615 · reported on NM_001012720
dbSNP: rs143761967
Type: single nucleotide variant
Location: chr10:84249003 (GRCh38)
Structure: AlphaFold pLDDT 62.88

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

Disease context

retinitis pigmentosa — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Retinitis pigmentosa (Orphanet):

Inheritance: Autosomal dominant, Autosomal recessive, Mitochondrial inheritance
Onset: Adolescent, Adult, Childhood
Prevalence: 1-5 / 10 000 (Europe)

Similar variants

RGR p.Ala234Thr Uncertain significance ★★ ⚠ same condition
RGR p.Arg289Gln Uncertain significance ★★ ⚠ same condition
RGR p.Asp154Asn Uncertain significance ★★ ⚠ same condition
RGR p.Gly87Ser Uncertain significance ★★ ⚠ same condition
RGR c.*416A>G Benign ★★ same condition
RGR c.*65A>G Benign ★★ same condition
RGR p.Ser241Phe Benign/Likely benign ★★ same condition
RGR p.Thr9= Benign ★★ same condition

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/rgr-p-ser106 (accessed [today's date]).

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