Is FANCD2 p.Phe704fs (c.2109_2110insGAGGT) pathogenic?

FANCD2 p.Phe704fs (c.21092110insGAGGT) is classified Pathogenic in FANCD2 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-05-22). Absent from gnomAD; Associated with Fanconi anemia.

What condition is associated with FANCD2 p.Phe704fs (c.2109_2110insGAGGT)?

FANCD2 p.Phe704fs (c.2109_2110insGAGGT) is associated with Fanconi anemia (ClinVar).

How common is FANCD2 p.Phe704fs (c.2109_2110insGAGGT) in the general population?

FANCD2 p.Phe704fs (c.2109_2110insGAGGT) is absent from gnomAD (gnomAD).

How is Hereditary isolated aplastic anemia inherited?

Typically Autosomal dominant, Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

FANCD2 p.Phe704fs

c.2109_2110insGAGGT · rs2469968584 · VCV2867038

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

Fanconi anemia

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 23 of 44
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -0.1	GERP -3.7, phastCons 0.015
Region caveats
Repeat context	seg dup	· reads may not map uniquely · confidence, not pathogenicity

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

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: FANCD2
Protein: p.Phe704fs
Coding: c.2109_2110insGAGGT
MANE Select: NM_001018115
dbSNP: rs2469968584
Type: Insertion
Location: chr3:10064816 (GRCh38)
Gene constraint: LOEUF 0.777 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 77.24 · 13 PDB
Residue 704: an α-helix

Full FANCD2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Fanconi anemia — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Hereditary isolated aplastic anemia (Orphanet):

Inheritance: Autosomal dominant, Autosomal recessive
Onset: Childhood

Similar variants

FANCD2 p.Arg401delinsPhePheValTer Pathogenic ★ same condition
FANCD2 p.Gln1053fs Pathogenic ★ same condition
FANCD2 p.Ile368fs Pathogenic ★ same condition
FANCD2 p.Pro1168fs Pathogenic ★ same condition
FANCD2 c.1948-6C>A Pathogenic/Likely pathogenic ★★ same condition
FANCD2 c.206-1G>T Likely pathogenic ★★ same condition
FANCD2 c.2169-1G>C Likely pathogenic ★★ same condition
FANCD2 c.2269+1G>A 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/fancd2-p-phe704fs (accessed [today's date]).

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