Is AAGAB p.Phe17= (c.51C>T) pathogenic?

AAGAB p.Phe17= (c.51C>T) is classified Benign in AAGAB (ClinVar, Single submitter, 1 submitter; last evaluated 2024-04-11). Rare (popmax 0.167%, afr).

How common is AAGAB p.Phe17= (c.51C>T) in the general population?

AAGAB p.Phe17= (c.51C>T) is rare (popmax 0.167%, afr) (gnomAD).

AAGAB p.Phe17=

c.51C>T · VCV3665421

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.167%, afr)

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 3.6	GERP 0.78, phastCons 1
Overall
CADD	9.41	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.167% African / African-American · 125/74,976 alleles

Filtering AF 0.143% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.134%

Overall 0.00801% 129/1,610,066 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.167%	600
Ashkenazi Jewishnot grpmax-eligible	0.00339%	29,524
Remaining individualsnot grpmax-eligible	0.00321%	31,111
Admixed American	0.00167%	59,798

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: AAGAB
Protein: p.Phe17=
Coding: c.51C>T
MANE Select: NM_024666
Type: single nucleotide variant
Location: chr15:67254581 (GRCh38)
Gene constraint: LOEUF 1.156 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 80.41 · 3 PDB
Residue 17: a β-strand

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

Similar variants

AAGAB p.Phe17Ser Uncertain significance ★ ⚠ same residue
AAGAB p.Phe17fs Likely pathogenic ★ same residue
AAGAB p.Arg124Ter Pathogenic ★★ same type
AAGAB p.Arg161Ter Pathogenic ★★ same type
AAGAB p.Gln21Ter Pathogenic ★★ same type
AAGAB p.Ala74Pro Uncertain significance ★★ ⚠ same type
AAGAB p.Arg161Gln Uncertain significance ★★ ⚠ same type
AAGAB p.Leu92Val 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/aagab-p-phe17 (accessed [today's date]).

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