Is FGF10 p.Pro34fs (c.101del) pathogenic?

FGF10 p.Pro34fs (c.101del) is classified Pathogenic in FGF10 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-06-25). Very rare (popmax 0.00167%, amr); Associated with lacrimoauriculodentodigital syndrome 3.

What condition is associated with FGF10 p.Pro34fs (c.101del)?

FGF10 p.Pro34fs (c.101del) is associated with lacrimoauriculodentodigital syndrome 3 (ClinVar).

How common is FGF10 p.Pro34fs (c.101del) in the general population?

FGF10 p.Pro34fs (c.101del) is very rare (popmax 0.00167%, amr) (gnomAD).

FGF10 p.Pro34fs

c.101del · rs1561223826 · VCV2009733

Pathogenic Multiple submitters

Classification

Pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 0.00167%, amr)

Conditions

lacrimoauriculodentodigital syndrome 3

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a haploinsufficient gene (ClinGen)
NMD	predicted	premature termination codon in exon 1 of 3
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 2.2	GERP -2.2, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00167% Admixed American · 1/60,026 alleles

Overall 6.84e-05% 1/1,461,888 alleles · very rare

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: FGF10
Protein: p.Pro34fs
Coding: c.101del
MANE Select: NM_004465
dbSNP: rs1561223826
Type: Deletion
Location: chr5:44388582 (GRCh38)
Gene constraint: LOEUF 0.267 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 81.12 · 2 PDB

Full FGF10 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

lacrimoauriculodentodigital syndrome 3 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

FGF10 p.Ser115_Val116insTer Likely pathogenic ★ same condition
FGF10 p.Pro34= Likely benign ★ same residue
FGF10 p.Val123Ile Uncertain significance ★★ ⚠ same condition
FGF10 p.Val205Met Uncertain significance ★★ ⚠ same condition
FGF10 p.Gly100Arg Likely pathogenic ★ same condition
FGF10 p.Tyr108Ter Likely pathogenic ★ same condition
FGF10 c.325+6T>C Uncertain significance ★ same condition
FGF10 p.Asn129Ser Uncertain significance ★ ⚠ 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/fgf10-p-pro34fs (accessed [today's date]).

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