Is OCRL p.His61= (c.183C>T) pathogenic?

OCRL p.His61= (c.183C>T) is classified Likely benign in OCRL (ClinVar, Single submitter, 1 submitter; last evaluated 2025-02-06). Ultra-rare (popmax 0.0109%, afr); Associated with oculocerebrorenal syndrome.

What condition is associated with OCRL p.His61= (c.183C>T)?

OCRL p.His61= (c.183C>T) is associated with oculocerebrorenal syndrome (ClinVar).

How common is OCRL p.His61= (c.183C>T) in the general population?

OCRL p.His61= (c.183C>T) is ultra-rare (popmax 0.0109%, afr) (gnomAD).

OCRL p.His61=

c.183C>T · rs1361099244 · VCV1910796

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0109%, afr)

Conditions

oculocerebrorenal syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal.
Splicing
SpliceAI	Δ0.27	donor loss · deltas
Constraint at this position
Conservation	phyloP 2.7	GERP 0.88, phastCons 1
Overall
CADD	8.591	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0109% African / African-American · 6/55,091 alleles

Filtering AF 0.0047% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00316%

Overall 0.000545% 6/1,101,638 alleles · ultra-rare exomes 3/989,332 · genomes 3/112,306 · joint denominator

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: OCRL
Protein: p.His61=
Coding: c.183C>T
MANE Select: NM_000276
dbSNP: rs1361099244
Type: single nucleotide variant
Location: chrX:129545021 (GRCh38)
Structure: AlphaFold pLDDT 82.91 · 5 PDB
Residue 61: the ph domain; a β-strand

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

Disease context

oculocerebrorenal syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

OCRL p.His61Arg Conflicting classifications of pathogenicity ★ ⚠ same residue
OCRL p.His61Tyr Uncertain significance ★ ⚠ same residue
OCRL c.1244+1G>A Pathogenic/Likely pathogenic ★★ same condition
OCRL c.1714-1G>A Pathogenic ★★ same condition
OCRL c.2256+1G>T Likely pathogenic ★★ same condition
OCRL c.560+1G>C Pathogenic/Likely pathogenic ★★ same condition
OCRL c.940-11G>A Pathogenic/Likely pathogenic ★★ same condition
OCRL p.Ala861Thr 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/ocrl-p-his61 (accessed [today's date]).

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