Is ATAD5 p.Pro13= (c.39G>C) pathogenic?

ATAD5 p.Pro13= (c.39G>C) is classified Benign in ATAD5 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-10-18). Common (popmax 49.1%, afr) — too common for a highly-penetrant pathogenic allele; Associated with ATAD5-related disorder.

What condition is associated with ATAD5 p.Pro13= (c.39G>C)?

ATAD5 p.Pro13= (c.39G>C) is associated with ATAD5-related disorder (ClinVar).

ATAD5 p.Pro13=

Q: How common is ATAD5 p.Pro13= (c.39G>C) in the general population?

ATAD5 p.Pro13= (c.39G>C) is common (popmax 49.1%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.39G>C · rs999796 · VCV3059114

Benign No assertion criteria

Classification

Benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Common

common (popmax 49.1%, afr) — too common for a highly-penetrant pathogenic allele

Conditions

ATAD5-related disorder

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 1.3	GERP 0.65, phastCons 1
Overall
CADD	13.67	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 49.1% African / African-American · 35,106/71,476 alleles

Filtering AF 48.7% ClinGen BA1/BS1 input FAF95, joint · FAF99 48.5%

Overall 14.3% 222,447/1,558,698 alleles · common

Ancestry group	Frequency	1 in
African / African-Americangrpmax	49.1%	2
South Asian	26.9%	4
Admixed American	19.7%	5
Amishnot grpmax-eligible	16.3%	6
East Asian	16%	6
Remaining individualsnot grpmax-eligible	15.3%	7
Middle Eastern	14.3%	7
European (non-Finnish)	11.2%	9
Ashkenazi Jewishnot grpmax-eligible	9.43%	11
Finnishnot grpmax-eligible	9.28%	11

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.Pro13=
Coding: c.39G>C
MANE Select: NM_024857
dbSNP: rs999796
Type: single nucleotide variant
Location: chr17:30832386 (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 p.Pro13Ala Uncertain significance ★ ⚠ same residue
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

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-pro13 (accessed [today's date]).

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