Is ADGRA3 p.Ala37= (c.111G>A) pathogenic?

ADGRA3 p.Ala37= (c.111G>A) is classified Likely benign in ADGRA3 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-10-20). Very rare (popmax 0.000532%, nfe).

How common is ADGRA3 p.Ala37= (c.111G>A) in the general population?

ADGRA3 p.Ala37= (c.111G>A) is very rare (popmax 0.000532%, nfe) (gnomAD).

ADGRA3 p.Ala37=

c.111G>A · rs1285250081 · VCV1376631

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.000532%, nfe)

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 -0.2	GERP -1.9
Overall
CADD	11.46	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000532% European (non-Finnish) · 5/939,026 alleles

Filtering AF 0.000156% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000113%

Overall 0.000433% 5/1,154,336 alleles · very rare

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: ADGRA3
Protein: p.Ala37=
Coding: c.111G>A
MANE Select: NM_145290
dbSNP: rs1285250081
Type: single nucleotide variant
Location: chr4:22515674 (GRCh38)
Gene constraint: LOEUF 0.607 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 70.20

Full ADGRA3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ADGRA3 p.Ala37Gly Uncertain significance ★★ ⚠ same residue
ADGRA3 p.Ala37Ser Uncertain significance ★ ⚠ same residue
ADGRA3 p.Ala37Val Uncertain significance ★ ⚠ same residue
ADGRA3 p.Ala1008Val Uncertain significance ★★ ⚠ same type
ADGRA3 p.Ala1120Val Uncertain significance ★★ ⚠ same type
ADGRA3 p.Ala1127Ser Uncertain significance ★★ ⚠ same type
ADGRA3 p.Ala177Val Uncertain significance ★★ ⚠ same type
ADGRA3 p.Ala26Pro 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/adgra3-p-ala37 (accessed [today's date]).

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