Is PALLD p.Asp964= (c.2892T>C) pathogenic?

PALLD p.Asp964= (c.2892T>C) is classified Benign/Likely benign in PALLD (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-07-20). Ultra-rare (popmax 0.0332%, mid); Associated with pancreatic adenocarcinoma.

What condition is associated with PALLD p.Asp964= (c.2892T>C)?

PALLD p.Asp964= (c.2892T>C) is associated with pancreatic adenocarcinoma (ClinVar).

How common is PALLD p.Asp964= (c.2892T>C) in the general population?

PALLD p.Asp964= (c.2892T>C) is ultra-rare (popmax 0.0332%, mid) (gnomAD).

PALLD p.Asp964=

c.2892T>C · rs140584890 · VCV697723

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0332%, mid)

Conditions

pancreatic adenocarcinoma

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.341	indeterminate
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -9.1	GERP -4.7
Overall
CADD	1.445	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0332% Middle Eastern · 2/6,028 alleles

Filtering AF 0.00585% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00314%

Overall 0.0129% 208/1,607,938 alleles · ultra-rare

Ancestry group	Frequency	1 in
Finnishnot grpmax-eligible	0.277%	360
Middle Easterngrpmax	0.0332%	3,014
South Asian	0.00885%	11,305
Remaining individualsnot grpmax-eligible	0.00802%	12,465
African / African-American	0.00274%	36,439
European (non-Finnish)	0.00127%	78,577

Finnish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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.Asp964=
Coding: c.2892T>C
MANE Select: NM_001166108
dbSNP: rs140584890
Type: single nucleotide variant
Location: chr4:168921575 (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-asp964 (accessed [today's date]).

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