Is PALLD p.Arg893= (c.2679A>G) pathogenic?

PALLD p.Arg893= (c.2679A>G) is classified Benign in PALLD (ClinVar, Multiple submitters, 7 submitters; last evaluated 2026-02-04). Common (popmax 20%, afr) — too common for a highly-penetrant pathogenic allele; Associated with pancreatic adenocarcinoma.

What condition is associated with PALLD p.Arg893= (c.2679A>G)?

PALLD p.Arg893= (c.2679A>G) is associated with pancreatic adenocarcinoma, pancreatic cancer, susceptibility to, 1 (ClinVar).

PALLD p.Arg893=

Q: How common is PALLD p.Arg893= (c.2679A>G) in the general population?

PALLD p.Arg893= (c.2679A>G) is common (popmax 20%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.2679A>G · rs1059444 · VCV348043

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 7 submitters

gnomAD v4.1

Common

common (popmax 20%, afr) — too common for a highly-penetrant pathogenic allele

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.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 0.87	GERP 1.1, phastCons 1
Overall
CADD	11.25	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 20% African / African-American · 14,945/74,884 alleles

Filtering AF 19.7% ClinGen BA1/BS1 input FAF95, joint · FAF99 19.6%

Overall 10.1% 162,484/1,611,468 alleles · common exomes 143,631/1,459,256 · genomes 18,853/152,212 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	20%	5
Ashkenazi Jewishnot grpmax-eligible	18.4%	5
Middle Eastern	14.6%	7
Remaining individualsnot grpmax-eligible	10.8%	9
European (non-Finnish)	10.2%	10
Amishnot grpmax-eligible	9.87%	10
Admixed American	8.27%	12
South Asian	5.18%	19
Finnishnot grpmax-eligible	4.94%	20
East Asian	4.16%	24

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.Arg893=
Coding: c.2679A>G
MANE Select: NM_001166108
dbSNP: rs1059444
Type: single nucleotide variant
Location: chr4:168913983 (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

Also linked: pancreatic cancer, susceptibility to, 1

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-arg893 (accessed [today's date]).

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