Is FANCD2 p.Gln320= (c.960A>G) pathogenic?

FANCD2 p.Gln320= (c.960A>G) is classified Uncertain significance in FANCD2 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-05-09). Absent from gnomAD v4.1; Associated with Fanconi anemia complementation group D2.

What condition is associated with FANCD2 p.Gln320= (c.960A>G)?

FANCD2 p.Gln320= (c.960A>G) is associated with Fanconi anemia complementation group D2 (ClinVar).

How common is FANCD2 p.Gln320= (c.960A>G) in the general population?

FANCD2 p.Gln320= (c.960A>G) is absent from gnomAD v4.1 (gnomAD).

FANCD2 p.Gln320=

c.960A>G · VCV3588164

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

Fanconi anemia complementation group D2

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal.
Splicing
SpliceAI	Δ0.92	donor gain · deltas
Pangolin	Δ0.82	gain · loss 0.57 · agrees with SpliceAI · independent
Constraint at this position
Conservation	phyloP 1.3	GERP 0.46, phastCons 1
Overall
CADD	18.09	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: FANCD2
Protein: p.Gln320=
Coding: c.960A>G
MANE Select: NM_001018115
Type: single nucleotide variant
Location: chr3:10043121 (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 320: the 'interaction with brca2' 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

Similar variants

FANCD2 p.Gln320Ter Pathogenic ★★ same residue
FANCD2 c.1279-1G>A Pathogenic/Likely pathogenic ★★ same condition
FANCD2 c.1279-2A>G Likely pathogenic ★★ same condition
FANCD2 c.1948-16T>G 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-gln320 (accessed [today's date]).

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