Is PALLD p.Thr992= (c.2976G>A) pathogenic?

PALLD p.Thr992= (c.2976G>A) is classified Likely benign in PALLD (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-08-06). Rare (popmax 0.102%, afr); Associated with pancreatic adenocarcinoma.

What condition is associated with PALLD p.Thr992= (c.2976G>A)?

PALLD p.Thr992= (c.2976G>A) is associated with pancreatic adenocarcinoma (ClinVar).

How common is PALLD p.Thr992= (c.2976G>A) in the general population?

PALLD p.Thr992= (c.2976G>A) is rare (popmax 0.102%, afr) (gnomAD).

PALLD p.Thr992=

c.2976G>A · rs143717202 · VCV416230

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

rare (popmax 0.102%, afr)

Conditions

pancreatic adenocarcinoma

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.04	moderately benign-leaning
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -20	GERP -4.7
Overall
CADD	0.058	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.102% African / African-American · 75/73,860 alleles

Filtering AF 0.083% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0762%

Overall 0.00615% 99/1,610,280 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.102%	985
Admixed American	0.0201%	4,969
Remaining individualsnot grpmax-eligible	0.0112%	8,904
European (non-Finnish)	0.000424%	235,879

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: PALLD
Protein: p.Thr992=
Coding: c.2976G>A
MANE Select: NM_032783 · reported on NM_001166108
dbSNP: rs143717202
Type: single nucleotide variant
Location: chr4:168921659 (GRCh38)

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

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-thr992 (accessed [today's date]).

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