Is OCRL p.Asp100fs (c.300del) pathogenic?

OCRL p.Asp100fs (c.300del) is classified Likely pathogenic in OCRL (ClinVar, Single submitter, 1 submitter; last evaluated 2022-03-17). No gnomAD frequency available for this variant; Associated with Dent disease type 2.

What condition is associated with OCRL p.Asp100fs (c.300del)?

OCRL p.Asp100fs (c.300del) is associated with Dent disease type 2 (ClinVar).

How common is OCRL p.Asp100fs (c.300del) in the general population?

OCRL p.Asp100fs (c.300del) is no gnomAD frequency available for this variant (gnomAD).

How is Dent disease inherited?

Typically X-linked recessive (Orphanet). A genetic counselor can assess individual risk for a family.

OCRL p.Asp100fs

c.300del · rs2521873170 · VCV3066348

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

Dent disease type 2

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a haploinsufficient gene (ClinGen)
NMD	predicted	premature termination codon in exon 5 of 24
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 11	GERP 1.9, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: OCRL
Protein: p.Asp100fs
Coding: c.300del
MANE Select: NM_000276
dbSNP: rs2521873170
Type: Deletion
Location: chrX:129557386 (GRCh38)
Structure: AlphaFold pLDDT 82.91 · 5 PDB
Residue 100: the ph domain

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

Disease context

Dent disease type 2 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Dent disease (Orphanet):

Inheritance: X-linked recessive
Onset: Childhood

Similar variants

OCRL p.Asn36fs Likely pathogenic ★ same condition
OCRL p.Gln38fs Likely pathogenic ★ same condition
OCRL p.Leu73fs Pathogenic ★ same condition
OCRL c.238+3_238+6del Uncertain significance ★ same condition
OCRL p.Arg884del Uncertain significance ★ same condition
OCRL p.Asp100Asn Uncertain significance ★ ⚠ same residue
OCRL p.Asp100Val Uncertain significance ★ ⚠ same residue
OCRL c.187_199+449del 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-asp100fs (accessed [today's date]).

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