Is DHTKD1 p.Arg888Ser (c.2662C>A) pathogenic?

DHTKD1 p.Arg888Ser (c.2662C>A) is classified Uncertain significance in DHTKD1 (ClinVar, Multiple submitters, 5 submitters; last evaluated 2025-12-17). AlphaMissense: likely benign (0.2298); Rare (popmax 0.132%, mid); Associated with Inborn genetic diseases.

What condition is associated with DHTKD1 p.Arg888Ser (c.2662C>A)?

DHTKD1 p.Arg888Ser (c.2662C>A) is associated with Inborn genetic diseases, 2-aminoadipic 2-oxoadipic aciduria (ClinVar).

How common is DHTKD1 p.Arg888Ser (c.2662C>A) in the general population?

DHTKD1 p.Arg888Ser (c.2662C>A) is rare (popmax 0.132%, mid) (gnomAD).

What do computational predictors say about DHTKD1 p.Arg888Ser (c.2662C>A)?

AlphaMissense predicts likely benign (score 0.2298) — an in-silico prediction, not a clinical call.

DHTKD1 p.Arg888Ser

c.2662C>A · rs143212640 · VCV858915

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 5 submitters

AlphaMissense

likely benign

0.2298 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.132%, mid)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.2298	likely benign
REVEL	0.18	moderately benign-leaning
SaProt	LLR -7.09	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Pangolin	Δ0.25	loss · gain 0.01 · not in the SpliceAI release · independent
Constraint at this position
Conservation	phyloP 2.7	GERP -0.17, phastCons 0.99
Regional constraint	o/e 1.05	unconstrained · MANE · 52 kb · p 0.072 · regional, not allelic
Overall
CADD	17.83	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.132% Middle Eastern · 8/6,058 alleles

Filtering AF 0.0657% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.048%

Overall 0.0115% 185/1,613,914 alleles · rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.132%	757
Ashkenazi Jewishnot grpmax-eligible	0.0608%	1,645
Admixed American	0.045%	2,223
African / African-American	0.044%	2,274
Remaining individualsnot grpmax-eligible	0.024%	4,166
European (non-Finnish)	0.00687%	14,566
South Asian	0.00329%	30,360

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: DHTKD1
Protein: p.Arg888Ser
Coding: c.2662C>A
MANE Select: NM_018706
dbSNP: rs143212640
Type: single nucleotide variant
Location: chr10:12120790 (GRCh38)
Gene constraint: LOEUF 0.864 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 95.19 · 8 PDB
Residue 888: a UniProt-annotated variant site (in aakad); a β-strand

Full DHTKD1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: 2-aminoadipic 2-oxoadipic aciduria

Similar variants

DHTKD1 p.Arg888Cys Uncertain significance ★★ ⚠ same residue
DHTKD1 p.Arg888His Uncertain significance ★★ ⚠ same residue
DHTKD1 p.Arg888Leu Uncertain significance ★ ⚠ same residue
DHTKD1 c.1671+1G>A Likely pathogenic ★★ same condition
DHTKD1 c.1897-1G>A Pathogenic/Likely pathogenic ★★ same condition
DHTKD1 c.2320-2A>T Likely pathogenic ★★ same condition
DHTKD1 c.2572+1G>A Likely pathogenic ★★ same condition
DHTKD1 p.Arg163Ter 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/dhtkd1-p-arg888ser (accessed [today's date]).

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