Is PALLD p.Lys660Ala (c.1978_1979delinsGC) pathogenic?

PALLD p.Lys660Ala (c.19781979delinsGC) is classified Uncertain significance in PALLD (ClinVar, Single submitter, 1 submitter; last evaluated 2023-01-18). No gnomAD frequency available for this variant; Associated with pancreatic adenocarcinoma.

What condition is associated with PALLD p.Lys660Ala (c.1978_1979delinsGC)?

PALLD p.Lys660Ala (c.1978_1979delinsGC) is associated with pancreatic adenocarcinoma (ClinVar).

How common is PALLD p.Lys660Ala (c.1978_1979delinsGC) in the general population?

PALLD p.Lys660Ala (c.1978_1979delinsGC) is no gnomAD frequency available for this variant (gnomAD).

PALLD p.Lys660Ala

c.1978_1979delinsGC · rs2533586570 · VCV2829948

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

pancreatic adenocarcinoma

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 11	GERP 1.3, phastCons 1
Regional constraint	o/e 0.99	unconstrained · MANE · 387 kb · p 0.73 · 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: PALLD
Protein: p.Lys660Ala
Coding: c.1978_1979delinsGC
MANE Select: NM_001166108
dbSNP: rs2533586570
Type: Indel
Location: chr4:168890935 (GRCh38)
Gene constraint: LOEUF 0.644 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 54.74 · 2 PDB
Residue 660: the 'interaction with lasp1' region

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

Disease context

pancreatic adenocarcinoma — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

PALLD p.Lys660del Uncertain significance ★★ same residue
PALLD c.1965-12625_1965-12624delinsGC Uncertain significance ★ same condition
PALLD c.1965-12772delinsCCGCCCC Uncertain significance ★ same condition
PALLD p.Lys660Gln Uncertain significance ★ same residue
PALLD p.Lys660Thr Uncertain significance ★ same residue
PALLD c.1965-12532C>A Uncertain significance ★★ same condition
PALLD c.1965-12532C>G Uncertain significance ★★ same condition
PALLD c.1965-12534C>A 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/palld-p-lys660ala (accessed [today's date]).

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