Is DDHD2 c.2054+13del pathogenic?

DDHD2 c.2054+13del is classified Likely benign in DDHD2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-04-10). Associated with hereditary spastic paraplegia 54.

What condition is associated with DDHD2 c.2054+13del?

DDHD2 c.2054+13del is associated with hereditary spastic paraplegia 54 (ClinVar).

How is Autosomal recessive spastic paraplegia type 54 inherited?

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

DDHD2 c.2054+13del

VCV4706163

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

Conditions

hereditary spastic paraplegia 54

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
Splice region	donor +13	near-intronic (+13 nt from the splice site)
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -1.2	GERP -3
Non-coding constraint	Z 2.53	1 kb window · o/e 0.81 · regional · uncalibrated

Variant & gene context

Gene: DDHD2
Coding: c.2054+13del
MANE Select: NM_015214
Type: Deletion
Location: chr8:38253729 (GRCh38)
Gene constraint: LOEUF 0.758 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 74.70

Full DDHD2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

hereditary spastic paraplegia 54 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Autosomal recessive spastic paraplegia type 54 (Orphanet):

Inheritance: Autosomal recessive
Onset: Childhood, Infancy

Similar variants

DDHD2 p.Lys124fs Pathogenic/Likely pathogenic ★★ same condition
DDHD2 p.Glu414fs Pathogenic ★ same condition
DDHD2 p.Gly344fs Likely pathogenic ★ same condition
DDHD2 p.Ile405_Phe406insTer Likely pathogenic ★ same condition
DDHD2 p.Lys152fs Pathogenic ★ same condition
DDHD2 p.Phe601fs Pathogenic ★ same condition
DDHD2 p.Tyr661fs Likely pathogenic ★ same condition
DDHD2 c.221-1_224del 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/ddhd2-c-2054-plus-13del (accessed [today's date]).

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