Is PALLD p.Ile987= (c.2961C>T) pathogenic?

PALLD p.Ile987= (c.2961C>T) is classified Conflicting classifications of pathogenicity in PALLD (ClinVar, Conflicting submitters, 2 submitters; last evaluated 2025-12-03). Very rare (popmax 0.0054%, afr); Associated with pancreatic adenocarcinoma.

What condition is associated with PALLD p.Ile987= (c.2961C>T)?

PALLD p.Ile987= (c.2961C>T) is associated with pancreatic adenocarcinoma (ClinVar).

How common is PALLD p.Ile987= (c.2961C>T) in the general population?

PALLD p.Ile987= (c.2961C>T) is very rare (popmax 0.0054%, afr) (gnomAD).

PALLD p.Ile987=

c.2961C>T · rs1484758238 · VCV1125873

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.0054%, afr)

Conditions

pancreatic adenocarcinoma

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.079	moderately benign-leaning
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 0.23	GERP 0.49, phastCons 0.97
Overall
CADD	12.89	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0054% African / African-American · 4/74,098 alleles

Filtering AF 0.00176% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00105%

Overall 0.000869% 14/1,611,330 alleles · very rare exomes 11/1,461,020 · genomes 3/150,310 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0054%	18,524
Remaining individualsnot grpmax-eligible	0.00481%	20,787
European (non-Finnish)	0.000593%	168,527

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.Ile987=
Coding: c.2961C>T
MANE Select: NM_001166108
dbSNP: rs1484758238
Type: single nucleotide variant
Location: chr4:168921644 (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-ile987 (accessed [today's date]).

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