Is DGKH p.Cys1007Arg (c.3019T>C) pathogenic?

DGKH p.Cys1007Arg (c.3019T>C) is classified Uncertain significance in DGKH (ClinVar, Single submitter, 1 submitter; last evaluated 2023-07-12). AlphaMissense: ambiguous (0.4872); No allele count reported in gnomAD v4.1 (AN 1,610,280).

How common is DGKH p.Cys1007Arg (c.3019T>C) in the general population?

DGKH p.Cys1007Arg (c.3019T>C) is no allele count reported in gnomAD v4.1 (AN 1,610,280) (gnomAD).

What do computational predictors say about DGKH p.Cys1007Arg (c.3019T>C)?

AlphaMissense predicts ambiguous (score 0.4872) — an in-silico prediction, not a clinical call.

DGKH p.Cys1007Arg

c.3019T>C · rs2138218647 · VCV2610926

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.4872 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,610,280)

Missense predictors

0/2 damaging

REVEL, SaProt · AlphaMissense indeterminate

Computational evidence

Protein change
AlphaMissense	0.4872	ambiguous
REVEL	0.151	moderately benign-leaning
SaProt	LLR -4.18	tolerated
⇒ REVEL and SaProt both call this tolerated; AlphaMissense is indeterminate.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · T>G here scores Δ0.59 · evaluated, not missing
Constraint at this position
Conservation	phyloP 7.9	GERP 1.7, phastCons 1
Regional constraint	o/e 0.68	unconstrained · MANE · 23 kb · p 6.1e-13 · regional, not allelic
Overall
CADD	21.3	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,610,280). 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: DGKH
Protein: p.Cys1007Arg
Coding: c.3019T>C
MANE Select: NM_178009
dbSNP: rs2138218647
Type: single nucleotide variant
Location: chr13:42214511 (GRCh38)
Gene constraint: LOEUF 0.689 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 71.33

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

Similar variants

DGKH p.Ala113Val Uncertain significance ★ ⚠ same type
DGKH p.Ala118Thr Uncertain significance ★ ⚠ same type
DGKH p.Ala19Ser Uncertain significance ★ ⚠ same type
DGKH p.Ala506Thr Uncertain significance ★ ⚠ same type
DGKH p.Ala627Thr Uncertain significance ★ ⚠ same type
DGKH p.Ala673Val Uncertain significance ★ ⚠ same type
DGKH p.Ala981Thr Uncertain significance ★ ⚠ same type
DGKH p.Ala985Thr Uncertain significance ★ ⚠ same type

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/dgkh-p-cys1007arg (accessed [today's date]).

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