Is DHDDS c.*480A>G pathogenic?

DHDDS c.480A>G is classified Uncertain significance in DHDDS (ClinVar, Single submitter, 1 submitter; last evaluated 2018-01-13). Low-frequency (popmax 1.4%, mid); Associated with retinitis pigmentosa.

What condition is associated with DHDDS c.*480A>G?

DHDDS c.*480A>G is associated with retinitis pigmentosa (ClinVar).

How common is DHDDS c.*480A>G in the general population?

DHDDS c.*480A>G is low-frequency (popmax 1.4%, mid) (gnomAD).

How is Retinitis pigmentosa inherited?

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

DHDDS c.*480A>G

rs552046225 · VCV297086

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

low-frequency (popmax 1.4%, mid)

Conditions

retinitis pigmentosa

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 3.1	GERP -2.3, phastCons 1
Non-coding constraint	Z 2.28	1 kb window · o/e 0.85 · regional · uncalibrated
Overall
CADD	9.828	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 1.4% Middle Eastern · 8/572 alleles

Filtering AF 0.696% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.548%

Overall 0.101% 236/234,314 alleles · low-frequency

Ancestry group	Frequency	1 in
Middle Easterngrpmax	1.4%	72
South Asian	0.686%	146
Admixed American	0.248%	403
Ashkenazi Jewishnot grpmax-eligible	0.205%	487
Remaining individualsnot grpmax-eligible	0.0964%	1,037
European (non-Finnish)	0.0322%	3,109
African / African-American	0.0134%	7,459

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: DHDDS
Coding: c.*480A>G
MANE Select: NM_205861
dbSNP: rs552046225
Type: single nucleotide variant
Location: chr1:26469611 (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 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Retinitis pigmentosa (Orphanet):

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

Similar variants

DHDDS p.Lys42Glu Pathogenic ★★ ⚠ same condition
DHDDS p.Thr206Ala Likely pathogenic ★★ same condition
DHDDS p.Arg265Gln Uncertain significance ★★ ⚠ same condition
DHDDS p.Arg298Pro Uncertain significance ★★ ⚠ same condition
DHDDS p.Arg306Gln Uncertain significance ★★ ⚠ same condition
DHDDS p.Asn18Ser Uncertain significance ★★ ⚠ same condition
DHDDS p.Gln53Glu Uncertain significance ★★ ⚠ same condition
DHDDS p.Leu282Pro 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-star-480a-g (accessed [today's date]).

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