Is DGKD p.Leu712= (c.2134C>T) pathogenic?

DGKD p.Leu712= (c.2134C>T) is classified Benign in DGKD (ClinVar, Single submitter, 2 submitters; last evaluated 2018-07-13). Rare (popmax 0.345%, afr).

How common is DGKD p.Leu712= (c.2134C>T) in the general population?

DGKD p.Leu712= (c.2134C>T) is rare (popmax 0.345%, afr) (gnomAD).

DGKD p.Leu712=

c.2134C>T · rs113452563 · VCV724328

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

rare (popmax 0.345%, afr)

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 1.3	GERP 0.028, phastCons 0.9
Overall
CADD	6.719	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.345% African / African-American · 259/75,022 alleles

Filtering AF 0.311% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.297%

Overall 0.0189% 304/1,612,108 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.345%	290
Middle Eastern	0.0661%	1,514
Admixed American	0.0317%	3,158
Remaining individualsnot grpmax-eligible	0.0208%	4,802
European (non-Finnish)	0.000764%	130,922

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: DGKD
Protein: p.Leu712=
Coding: c.2134C>T
MANE Select: NM_152879
dbSNP: rs113452563
Type: single nucleotide variant
Location: chr2:233451017 (GRCh38)
Gene constraint: LOEUF 0.547 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 72.02 · 2 PDB

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

Similar variants

DGKD c.2375+10A>G Benign ★★ same type
DGKD p.Leu406= Benign ★★ same type
DGKD p.Pro568= Benign/Likely benign ★★ same type
DGKD p.Thr1052= Benign ★★ same type
DGKD p.Ala1047Gly Uncertain significance ★ ⚠ same type
DGKD p.Ala1109Val Uncertain significance ★ ⚠ same type
DGKD p.Ala1134Val Uncertain significance ★ ⚠ same type
DGKD p.Ala1140Gly 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/dgkd-p-leu712 (accessed [today's date]).

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