Is DHDDS c.*2104A>T pathogenic?

DHDDS c.2104A>T is classified Uncertain significance in DHDDS (ClinVar, Single submitter, 1 submitter; last evaluated 2018-01-12). Rare (popmax 0.34%, mid); Associated with retinitis pigmentosa.

What condition is associated with DHDDS c.*2104A>T?

DHDDS c.*2104A>T is associated with retinitis pigmentosa (ClinVar).

How common is DHDDS c.*2104A>T in the general population?

DHDDS c.*2104A>T is rare (popmax 0.34%, 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.*2104A>T

rs182595109 · VCV297109

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.34%, 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 -0.55	GERP -3.6
Non-coding constraint	Z -0.22	1 kb window · o/e 1.01 · regional · uncalibrated
Overall
CADD	4.753	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.34% Middle Eastern · 1/294 alleles

Filtering AF 0.103% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.087%

Overall 0.0328% 50/152,344 alleles · rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.34%	294
Remaining individualsnot grpmax-eligible	0.188%	531
Admixed American	0.15%	665
European (non-Finnish)	0.0235%	4,252
African / African-American	0.0144%	6,931

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.*2104A>T
MANE Select: NM_205861
dbSNP: rs182595109
Type: single nucleotide variant
Location: chr1:26471235 (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-2104a-t (accessed [today's date]).

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