Is FH p.Ala9= (c.27G>A) pathogenic?

FH p.Ala9= (c.27G>A) is classified Benign/Likely benign in FH (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-12-15). Very rare (popmax 0.00137%, afr); Associated with hereditary neoplastic syndrome.

What condition is associated with FH p.Ala9= (c.27G>A)?

FH p.Ala9= (c.27G>A) is associated with hereditary neoplastic syndrome, hereditary leiomyomatosis and renal cell cancer (ClinVar).

How common is FH p.Ala9= (c.27G>A) in the general population?

FH p.Ala9= (c.27G>A) is very rare (popmax 0.00137%, afr) (gnomAD).

FH p.Ala9=

c.27G>A · rs983362570 · VCV460349

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00137%, afr)

Conditions

hereditary neoplastic syndrome

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 0.28	GERP 1.9, phastCons 0.87
Overall
CADD	12.67	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00137% African / African-American · 1/72,798 alleles

Filtering AF 0.000254% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000163%

Overall 0.000517% 8/1,546,598 alleles · very rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00137%	72,798
European (non-Finnish)	0.000611%	163,685

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: FH
Protein: p.Ala9=
Coding: c.27G>A
MANE Select: NM_000143
dbSNP: rs983362570
Type: single nucleotide variant
Location: chr1:241519696 (GRCh38)
Gene constraint: LOEUF 0.599 · pLI 0.27 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 92.92 · 8 PDB

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

Disease context

hereditary neoplastic syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: hereditary leiomyomatosis and renal cell cancer

Similar variants

FH p.Ala9Val Uncertain significance ★★ ⚠ same residue
FH p.Ala9Gly Conflicting classifications of pathogenicity ★ ⚠ same residue
FH p.Ala9Thr Uncertain significance ★ ⚠ same residue
FH p.Ala9_Leu14dup Conflicting classifications of pathogenicity ★ same residue
FH p.Ala9fs Uncertain significance ★ same residue
FH c.1108+1G>A Pathogenic ★★ same condition
FH c.1108+1G>T Pathogenic/Likely pathogenic ★★ same condition
FH c.1236+1G>A Pathogenic/Likely pathogenic ★★ 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/fh-p-ala9 (accessed [today's date]).

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