Is ADCY10 p.Leu802= (c.2406G>A) pathogenic?

ADCY10 p.Leu802= (c.2406G>A) is classified Likely benign in ADCY10 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2024-12-23). Ultra-rare (popmax 0.1%, afr); Associated with hypercalciuria, absorptive, 2.

What condition is associated with ADCY10 p.Leu802= (c.2406G>A)?

ADCY10 p.Leu802= (c.2406G>A) is associated with hypercalciuria, absorptive, 2 (ClinVar).

How common is ADCY10 p.Leu802= (c.2406G>A) in the general population?

ADCY10 p.Leu802= (c.2406G>A) is ultra-rare (popmax 0.1%, afr) (gnomAD).

ADCY10 p.Leu802=

c.2406G>A · rs201086008 · VCV1570599

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.1%, afr)

Conditions

hypercalciuria, absorptive, 2

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 0.98	GERP 0.73, phastCons 1
Overall
CADD	2.657	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.1% African / African-American · 75/75,018 alleles

Filtering AF 0.0817% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.075%

Overall 0.00558% 90/1,613,986 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.1%	1,000
Admixed American	0.0167%	6,002
Remaining individualsnot grpmax-eligible	0.0064%	15,624
European (non-Finnish)	8.48e-05%	1,179,933

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: ADCY10
Protein: p.Leu802=
Coding: c.2406G>A
MANE Select: NM_018417
dbSNP: rs201086008
Type: single nucleotide variant
Location: chr1:167848392 (GRCh38)
Gene constraint: LOEUF 0.922 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 81.17 · 37 PDB

Full ADCY10 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

hypercalciuria, absorptive, 2 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

ADCY10 p.Leu802Met Uncertain significance ★★ ⚠ same residue
ADCY10 c.1139+6T>G Uncertain significance ★★ same condition
ADCY10 c.253+4A>G Uncertain significance ★★ same condition
ADCY10 p.Ala103Ser Uncertain significance ★★ ⚠ same condition
ADCY10 p.Arg1588Thr Uncertain significance ★★ ⚠ same condition
ADCY10 p.Asn1081Lys Uncertain significance ★★ ⚠ same condition
ADCY10 p.Asp704Gly Uncertain significance ★★ ⚠ same condition
ADCY10 p.Cys1141Ser Uncertain significance ★★ ⚠ 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/adcy10-p-leu802 (accessed [today's date]).

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