Is ATP6V0A2 p.Val699= (c.2097T>A) pathogenic?

ATP6V0A2 p.Val699= (c.2097T>A) is classified Likely benign in ATP6V0A2 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-11-19). Very rare (popmax 0.00167%, amr); Associated with ALG9-congenital disorder of glycosylation.

What condition is associated with ATP6V0A2 p.Val699= (c.2097T>A)?

ATP6V0A2 p.Val699= (c.2097T>A) is associated with ALG9-congenital disorder of glycosylation (ClinVar).

How common is ATP6V0A2 p.Val699= (c.2097T>A) in the general population?

ATP6V0A2 p.Val699= (c.2097T>A) is very rare (popmax 0.00167%, amr) (gnomAD).

How is ALG9-CDG inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

ATP6V0A2 p.Val699=

c.2097T>A · rs1956723735 · VCV3020167

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00167%, amr)

Conditions

ALG9-congenital disorder of glycosylation

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 -3.2	GERP -3.5
Overall
CADD	0.495	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00167% Admixed American · 1/60,024 alleles

Filtering AF 0.000124% ClinGen BA1/BS1 input FAF95, joint · FAF99 9e-05%

Overall 0.00041% 6/1,461,846 alleles · very rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00167%	60,024
European (non-Finnish)	0.000424%	236,004

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: ATP6V0A2
Protein: p.Val699=
Coding: c.2097T>A
MANE Select: NM_012463
dbSNP: rs1956723735
Type: single nucleotide variant
Location: chr12:123752324 (GRCh38)
Gene constraint: LOEUF 0.603 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 81.94

Full ATP6V0A2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

ALG9-congenital disorder of glycosylation — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For ALG9-CDG (Orphanet):

Inheritance: Autosomal recessive
Onset: Antenatal, Infancy, Neonatal

Similar variants

ATP6V0A2 c.1514+1G>A Pathogenic/Likely pathogenic ★★ same condition
ATP6V0A2 c.1724+2T>C Likely pathogenic ★★ same condition
ATP6V0A2 c.2293+1G>A Likely pathogenic ★★ same condition
ATP6V0A2 c.732-2A>G Pathogenic ★★ same condition
ATP6V0A2 p.Ala397Pro Likely pathogenic ★★ same condition
ATP6V0A2 p.Arg526Ter Pathogenic ★★ same condition
ATP6V0A2 p.Arg63Ter Pathogenic ★★ same condition
ATP6V0A2 p.Gln70Ter Pathogenic/Likely pathogenic ★★ 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/atp6v0a2-p-val699 (accessed [today's date]).

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