Is ATAD5 p.Ser925= (c.2775C>T) pathogenic?

ATAD5 p.Ser925= (c.2775C>T) is classified Likely benign in ATAD5 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-07-10). Ultra-rare (popmax 0.0953%, amr); Associated with ATAD5-related disorder.

What condition is associated with ATAD5 p.Ser925= (c.2775C>T)?

ATAD5 p.Ser925= (c.2775C>T) is associated with ATAD5-related disorder (ClinVar).

How common is ATAD5 p.Ser925= (c.2775C>T) in the general population?

ATAD5 p.Ser925= (c.2775C>T) is ultra-rare (popmax 0.0953%, amr) (gnomAD).

ATAD5 p.Ser925=

c.2775C>T · rs758984843 · VCV3049297

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0953%, amr)

Conditions

ATAD5-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · C>A here scores Δ0.31 · evaluated, not missing
Constraint at this position
Conservation	phyloP -0.3	GERP -2.9
Overall
CADD	7.638	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0953% Admixed American · 56/58,768 alleles

Filtering AF 0.0753% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0682%

Overall 0.00416% 67/1,610,644 alleles · ultra-rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0953%	1,049
African / African-American	0.00134%	74,682
European (non-Finnish)	0.000848%	117,938

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: ATAD5
Protein: p.Ser925=
Coding: c.2775C>T
MANE Select: NM_024857
dbSNP: rs758984843
Type: single nucleotide variant
Location: chr17:30857094 (GRCh38)
Gene constraint: LOEUF 0.417 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 46.76 · 4 PDB

Full ATAD5 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

ATAD5-related disorder

Similar variants

ATAD5 c.2956+9T>C Likely benign same condition
ATAD5 c.5456+7G>C Benign same condition
ATAD5 c.5457-7T>G Likely benign same condition
ATAD5 p.Arg1448Cys Benign same condition
ATAD5 p.Arg249Lys Benign same condition
ATAD5 p.Arg52= Likely benign same condition
ATAD5 p.Asn1767Ser Benign same condition
ATAD5 p.Asn699His Benign 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/atad5-p-ser925 (accessed [today's date]).

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