Is FANCD2 p.Lys13fs (c.38_39del) pathogenic?

FANCD2 p.Lys13fs (c.3839del) is classified Pathogenic in FANCD2 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-08-25). Absent from gnomAD; Associated with Fanconi anemia complementation group D2.

What condition is associated with FANCD2 p.Lys13fs (c.38_39del)?

FANCD2 p.Lys13fs (c.38_39del) is associated with Fanconi anemia complementation group D2, Fanconi anemia (ClinVar).

How common is FANCD2 p.Lys13fs (c.38_39del) in the general population?

FANCD2 p.Lys13fs (c.38_39del) is absent from gnomAD (gnomAD).

FANCD2 p.Lys13fs

c.38_39del · rs1575723664 · VCV2982057

Pathogenic Multiple submitters

Classification

Pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

Fanconi anemia complementation group D2

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 2 of 44
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -0.089	GERP 0.23, phastCons 0.85

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.Lys13fs
Coding: c.38_39del
MANE Select: NM_001018115
dbSNP: rs1575723664
Type: Deletion
Location: chr3:10028694 (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 13: the 'interaction with fance' region; the 'disordered' region

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

Disease context

Fanconi anemia complementation group D2 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: Fanconi anemia

Similar variants

FANCD2 p.Lys13Arg Uncertain significance ★★ ⚠ same residue
FANCD2 c.2609_2613del Pathogenic/Likely pathogenic ★★ same condition
FANCD2 p.Asn1032fs Likely pathogenic ★★ same condition
FANCD2 p.Gln1100fs Pathogenic/Likely pathogenic ★★ same condition
FANCD2 p.Glu888fs Pathogenic ★★ same condition
FANCD2 p.Gly1101fs Likely pathogenic ★★ same condition
FANCD2 p.His654fs Pathogenic/Likely pathogenic ★★ same condition
FANCD2 p.Ile945_Leu946insTer 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/fancd2-p-lys13fs (accessed [today's date]).

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