Is ADAT3 p.Pro236Ser (c.706C>T) pathogenic?

ADAT3 p.Pro236Ser (c.706C>T) is classified Uncertain significance in ADAT3 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-03-11). Very rare (popmax 0.00187%, amr); Associated with Inborn genetic diseases.

What condition is associated with ADAT3 p.Pro236Ser (c.706C>T)?

ADAT3 p.Pro236Ser (c.706C>T) is associated with Inborn genetic diseases (ClinVar).

How common is ADAT3 p.Pro236Ser (c.706C>T) in the general population?

ADAT3 p.Pro236Ser (c.706C>T) is very rare (popmax 0.00187%, amr) (gnomAD).

ADAT3 p.Pro236Ser

c.706C>T · rs1406445412 · VCV2402604

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00187%, amr)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.391	indeterminate
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 5.6	GERP 0.11, phastCons 1
Regional constraint	o/e 1.29	unconstrained · MANE · 1,100 bp · p 7.8e-12 · regional, not allelic
Overall
CADD	23.8	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00187% Admixed American · 1/53,586 alleles

Overall 0.000143% 2/1,399,136 alleles · very rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00187%	53,586
European (non-Finnish)	8.65e-05%	1,156,426

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: ADAT3
Protein: p.Pro236Ser
Coding: c.706C>T
MANE Select: NM_138422
dbSNP: rs1406445412
Type: single nucleotide variant
Location: chr19:1912753 (GRCh38)
Gene constraint: LOEUF 1.929 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 88.83
Residue 236: the cmp/dcmp-type deaminase domain

Full ADAT3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

ADAT3 p.Leu247Val Uncertain significance ★★ same condition
ADAT3 p.Pro292Leu Uncertain significance ★★ same condition
ADAT3 p.Val223Met Uncertain significance ★★ same condition
ADAT3 p.Asp285Ala Likely benign ★★ same condition
ADAT3 p.Ala105Gly Uncertain significance ★ same condition
ADAT3 p.Ala146Thr Uncertain significance ★ same condition
ADAT3 p.Ala146Val Uncertain significance ★ same condition
ADAT3 p.Ala177Thr 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/adat3-p-pro236ser (accessed [today's date]).

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