Is ADGRD1 p.Lys444= (c.1332G>A) pathogenic?

ADGRD1 p.Lys444= (c.1332G>A) is classified Likely benign in ADGRD1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-10-08). Absent from gnomAD v4.1.

How common is ADGRD1 p.Lys444= (c.1332G>A) in the general population?

ADGRD1 p.Lys444= (c.1332G>A) is absent from gnomAD v4.1 (gnomAD).

ADGRD1 p.Lys444=

c.1332G>A · VCV4638196

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

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 8.2	GERP 0.97, phastCons 1
Overall
CADD	12.54	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: ADGRD1
Protein: p.Lys444=
Coding: c.1332G>A
MANE Select: NM_198827
Type: single nucleotide variant
Location: chr12:131014199 (GRCh38)
Gene constraint: LOEUF 0.826 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 72.06 · 8 PDB
Residue 444: the gain-b domain

Full ADGRD1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ADGRD1 p.Pro165Ala Uncertain significance ★★ ⚠ same type
ADGRD1 p.Ala124Thr Uncertain significance ★ ⚠ same type
ADGRD1 p.Ala124Val Uncertain significance ★ ⚠ same type
ADGRD1 p.Ala381Ser Uncertain significance ★ ⚠ same type
ADGRD1 p.Ala40Val Uncertain significance ★ ⚠ same type
ADGRD1 p.Ala565Val Uncertain significance ★ ⚠ same type
ADGRD1 p.Ala648Val Uncertain significance ★ ⚠ same type
ADGRD1 p.Ala709Val 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/adgrd1-p-lys444 (accessed [today's date]).

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