Is DAGLA p.Ile4= (c.12C>T) pathogenic?

DAGLA p.Ile4= (c.12C>T) is classified Likely benign in DAGLA (ClinVar, No assertion criteria, 1 submitter; last evaluated 2020-01-10). Rare (popmax 0.128%, nfe); Associated with DAGLA-related disorder.

What condition is associated with DAGLA p.Ile4= (c.12C>T)?

DAGLA p.Ile4= (c.12C>T) is associated with DAGLA-related disorder (ClinVar).

How common is DAGLA p.Ile4= (c.12C>T) in the general population?

DAGLA p.Ile4= (c.12C>T) is rare (popmax 0.128%, nfe) (gnomAD).

DAGLA p.Ile4=

c.12C>T · rs142265242 · VCV3052577

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.128%, nfe)

Conditions

DAGLA-related disorder

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 -4.6	GERP -0.77
Overall
CADD	9.626	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.128% European (non-Finnish) · 1,514/1,180,026 alleles

Filtering AF 0.123% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.121%

Overall 0.0999% 1,611/1,612,976 alleles · rare exomes 1,507/1,460,772 · genomes 104/152,204 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.128%	779
Remaining individualsnot grpmax-eligible	0.0544%	1,838
Finnishnot grpmax-eligible	0.0334%	2,998
African / African-American	0.0267%	3,746
Admixed American	0.0167%	6,000
South Asian	0.0132%	7,591

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: DAGLA
Protein: p.Ile4=
Coding: c.12C>T
MANE Select: NM_006133
dbSNP: rs142265242
Type: single nucleotide variant
Location: chr11:61720167 (GRCh38)
Gene constraint: LOEUF 0.305 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 63.87

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

Disease context

DAGLA-related disorder

Similar variants

DAGLA p.Met286Leu Uncertain significance ⚠ same condition
DAGLA p.Pro333Leu Uncertain significance ⚠ same condition
DAGLA c.1657-4G>A Likely benign same condition
DAGLA c.1983+10C>T Benign same condition
DAGLA p.Ala508= Benign same condition
DAGLA p.Ala748= Likely benign same condition
DAGLA p.Ala749Val Likely benign same condition
DAGLA p.Arg82= Likely benign 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/dagla-p-ile4 (accessed [today's date]).

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