Is ACOT7 p.Phe102= (c.306C>T) pathogenic?

ACOT7 p.Phe102= (c.306C>T) is classified Likely benign in ACOT7 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-05-28). Rare (popmax 0.195%, afr); Associated with ACOT7-related disorder.

What condition is associated with ACOT7 p.Phe102= (c.306C>T)?

ACOT7 p.Phe102= (c.306C>T) is associated with ACOT7-related disorder (ClinVar).

How common is ACOT7 p.Phe102= (c.306C>T) in the general population?

ACOT7 p.Phe102= (c.306C>T) is rare (popmax 0.195%, afr) (gnomAD).

ACOT7 p.Phe102=

c.306C>T · rs147559738 · VCV3039510

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.195%, afr)

Conditions

ACOT7-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 5.6	GERP 2.4, phastCons 1
Overall
CADD	11.98	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.195% African / African-American · 146/75,058 alleles

Filtering AF 0.169% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.159%

Overall 0.0117% 188/1,613,602 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.195%	514
East Asian	0.0267%	3,740
Remaining individualsnot grpmax-eligible	0.024%	4,167
Admixed American	0.0167%	6,003
South Asian	0.0011%	91,084
European (non-Finnish)	0.000339%	295,004

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: ACOT7
Protein: p.Phe102=
Coding: c.306C>T
MANE Select: NM_007274
dbSNP: rs147559738
Type: single nucleotide variant
Location: chr1:6339545 (GRCh38)
Gene constraint: LOEUF 0.468 · pLI 0.99 (gnomAD)
Structure: AlphaFold pLDDT 85.06 · 1 PDB
Residue 102: the hotdog acot-type 1 domain

Full ACOT7 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

ACOT7-related disorder

Similar variants

ACOT7 c.143+7755T>C Likely benign same condition
ACOT7 c.144-10787G>A Likely benign same condition
ACOT7 c.144-8956C>T Benign same condition
ACOT7 p.Thr341= Benign same condition
ACOT7 p.Val128= Benign same condition
ACOT7 p.Asp266= Benign ★★ same type
ACOT7 c.143+7600C>T Uncertain significance ★ ⚠ same type
ACOT7 c.143+7603G>T 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/acot7-p-phe102 (accessed [today's date]).

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