Is PRPF31 p.Pro245= (c.735C>T) pathogenic?

PRPF31 p.Pro245= (c.735C>T) is classified Benign in PRPF31 (ClinVar, Multiple submitters, 6 submitters; last evaluated 2026-02-03). Common (popmax 10.7%, sas) — too common for a highly-penetrant pathogenic allele; Associated with retinitis pigmentosa 11.

What condition is associated with PRPF31 p.Pro245= (c.735C>T)?

PRPF31 p.Pro245= (c.735C>T) is associated with retinitis pigmentosa 11, inherited retinal dystrophy, retinitis pigmentosa (ClinVar).

How is Retinitis pigmentosa inherited?

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

PRPF31 p.Pro245=

Q: How common is PRPF31 p.Pro245= (c.735C>T) in the general population?

PRPF31 p.Pro245= (c.735C>T) is common (popmax 10.7%, sas) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.735C>T · rs11556769 · VCV330100

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 6 submitters

gnomAD v4.1

Common

common (popmax 10.7%, sas) — too common for a highly-penetrant pathogenic allele

Conditions

retinitis pigmentosa 11

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 -9.2	GERP -3.1
Overall
CADD	7.61	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 10.7% South Asian · 9,746/91,060 alleles

Filtering AF 10.5% ClinGen BA1/BS1 input FAF95, joint · FAF99 10.5%

Overall 9.57% 154,203/1,611,194 alleles · common

Ancestry group	Frequency	1 in
South Asiangrpmax	10.7%	9
European (non-Finnish)	10.3%	10
Finnishnot grpmax-eligible	9.62%	10
Remaining individualsnot grpmax-eligible	9.47%	11
Middle Eastern	8.3%	12
African / African-American	6.62%	15
Ashkenazi Jewishnot grpmax-eligible	6.36%	16
Admixed American	6.24%	16
Amishnot grpmax-eligible	2.08%	48
East Asian	0.274%	365

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: PRPF31
Protein: p.Pro245=
Coding: c.735C>T
MANE Select: NM_015629
dbSNP: rs11556769
Type: single nucleotide variant
Location: chr19:54124536 (GRCh38)
Gene constraint: LOEUF 0.347 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 77.69 · 30 PDB
Residue 245: the nop domain

Full PRPF31 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

retinitis pigmentosa 11 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: inherited retinal dystrophy retinitis pigmentosa

For Retinitis pigmentosa (Orphanet):

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

Similar variants

PRPF31 c.1074-1G>C Likely pathogenic ★★ same condition
PRPF31 c.1074-2A>G Pathogenic ★★ same condition
PRPF31 c.1074-2A>T Pathogenic ★★ same condition
PRPF31 c.1146+5G>T Likely pathogenic ★★ same condition
PRPF31 c.1374+654C>G Pathogenic ★★ same condition
PRPF31 c.178-2A>G Pathogenic ★★ same condition
PRPF31 c.238+1G>A Pathogenic ★★ same condition
PRPF31 c.239-1G>A Pathogenic/Likely pathogenic ★★ 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/prpf31-p-pro245 (accessed [today's date]).

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