Is FGFR2 p.Ala172Phe (c.514_515delinsTT) pathogenic?

FGFR2 p.Ala172Phe (c.514515delinsTT) is classified Likely pathogenic in FGFR2 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-03-03). No gnomAD frequency available for this variant.

How common is FGFR2 p.Ala172Phe (c.514_515delinsTT) in the general population?

FGFR2 p.Ala172Phe (c.514_515delinsTT) is no gnomAD frequency available for this variant (gnomAD).

FGFR2 p.Ala172Phe

c.514_515delinsTT · rs2540580216 · VCV2578102

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 12	GERP 0.91, phastCons 1
Regional constraint	o/e 0.50	unconstrained · MANE · 34 kb · p 7.3e-17 · regional, not allelic

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: FGFR2
Protein: p.Ala172Phe
Coding: c.514_515delinsTT
MANE Select: NM_000141
dbSNP: rs2540580216
Type: Indel
Location: chr10:121551399 (GRCh38)
Gene constraint: LOEUF 0.278 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 74.33 · 65 PDB
Residue 172: the 'heparin-binding' region; a UniProt-annotated variant site (in ps; requires 2 nucleotide substitutions); the ig-like c2-type 2 domain

Full FGFR2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

FGFR2 c.1562-9_1562-7delinsAA Uncertain significance ★★ same type
FGFR2 p.Ala355_Val359delinsValTrpLeuThrIle Pathogenic ★ same type
FGFR2 p.Asn549Leu Likely pathogenic ★ same type
FGFR2 p.Cys278Leu Likely pathogenic ★ same type
FGFR2 p.Cys342Gly Pathogenic ★ same type
FGFR2 p.Ser252Phe Likely pathogenic ★ same type
FGFR2 p.Tyr586Ter Likely pathogenic ★ same type
FGFR2 c.1562-9_1562-8delinsAA 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/fgfr2-p-ala172phe (accessed [today's date]).

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