Is ATAD3A p.Ser120= (c.360C>T) pathogenic?

ATAD3A p.Ser120= (c.360C>T) is classified Likely benign in ATAD3A (ClinVar, Multiple submitters, 4 submitters; last evaluated 2026-07-01). Ultra-rare (popmax 0.0371%, nfe).

How common is ATAD3A p.Ser120= (c.360C>T) in the general population?

ATAD3A p.Ser120= (c.360C>T) is ultra-rare (popmax 0.0371%, nfe) (gnomAD).

ATAD3A p.Ser120=

c.360C>T · rs571690031 · VCV1012719

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0371%, 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 -13	GERP -2.6
Overall
CADD	2.11	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0371% European (non-Finnish) · 422/1,138,618 alleles

Filtering AF 0.0341% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.033%

Overall 0.033% 504/1,526,378 alleles · ultra-rare

Ancestry group	Frequency	1 in
Ashkenazi Jewishnot grpmax-eligible	0.0596%	1,677
European (non-Finnish)grpmax	0.0371%	2,698
Admixed American	0.0328%	3,050
Remaining individualsnot grpmax-eligible	0.0321%	3,114
South Asian	0.0257%	3,897
Middle Eastern	0.0231%	4,338
East Asian	0.00756%	13,223
African / African-American	0.00601%	16,632
Finnishnot grpmax-eligible	0.00172%	58,052

Ashkenazi Jewish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: ATAD3A
Protein: p.Ser120=
Coding: c.360C>T
MANE Select: NM_001170535
dbSNP: rs571690031
Type: single nucleotide variant
Location: chr1:1517388 (GRCh38)
Gene constraint: LOEUF 0.861 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 82.35
Residue 120: the 'disordered' region

Full ATAD3A gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ATAD3A c.1266+1G>A Likely pathogenic ★★ same type
ATAD3A c.384+1G>A Likely pathogenic ★★ same type
ATAD3A p.Arg528Gln Likely pathogenic ★★ ⚠ same type
ATAD3A p.Arg528Trp Pathogenic/Likely pathogenic ★★ ⚠ same type
ATAD3A c.282+5G>A Uncertain significance ★★ same type
ATAD3A c.283-3C>T Uncertain significance ★★ same type
ATAD3A c.385-3C>G Uncertain significance ★★ same type
ATAD3A p.Ala462Thr 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/atad3a-p-ser120 (accessed [today's date]).

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