Is DHDDS c.63+11del pathogenic?

DHDDS c.63+11del is classified Likely benign in DHDDS (ClinVar, Single submitter, 1 submitter; last evaluated 2024-11-18). Absent from gnomAD; Associated with retinitis pigmentosa 59.

What condition is associated with DHDDS c.63+11del?

DHDDS c.63+11del is associated with retinitis pigmentosa 59 (ClinVar).

How common is DHDDS c.63+11del in the general population?

DHDDS c.63+11del is absent from gnomAD (gnomAD).

DHDDS c.63+11del

rs2124329873 · VCV1640266

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

retinitis pigmentosa 59

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
Splice region	donor +11	near-intronic (+11 nt from the splice site)
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -0.44	GERP -0.92

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: DHDDS
Coding: c.63+11del
MANE Select: NM_205861
dbSNP: rs2124329873
Type: Deletion
Location: chr1:26433018 (GRCh38)
Gene constraint: LOEUF 0.536 · pLI 0.91 (gnomAD)
Structure: AlphaFold pLDDT 95.01 · 9 PDB

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

Disease context

retinitis pigmentosa 59 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

DHDDS p.His222fs Likely pathogenic ★★ same condition
DHDDS p.Ser88fs Pathogenic/Likely pathogenic ★★ same condition
DHDDS c.650_657+54del Likely pathogenic ★ same condition
DHDDS p.Asp34fs Pathogenic ★ same condition
DHDDS p.Phe215fs Likely pathogenic ★ same condition
DHDDS p.Thr276fs Likely pathogenic ★ same condition
DHDDS c.323+2_323+5del Conflicting classifications of pathogenicity ★ ⚠ same condition
DHDDS c.766-4del Uncertain significance ★ 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/dhdds-c-63-plus-11del (accessed [today's date]).

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