Is PALLD p.Ser1111= (c.3333C>T) pathogenic?

PALLD p.Ser1111= (c.3333C>T) is classified Likely benign in PALLD (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-07-22). Very rare (popmax 0.005%, amr); Associated with pancreatic adenocarcinoma.

What condition is associated with PALLD p.Ser1111= (c.3333C>T)?

PALLD p.Ser1111= (c.3333C>T) is associated with pancreatic adenocarcinoma (ClinVar).

How common is PALLD p.Ser1111= (c.3333C>T) in the general population?

PALLD p.Ser1111= (c.3333C>T) is very rare (popmax 0.005%, amr) (gnomAD).

PALLD p.Ser1111=

c.3333C>T · rs1762303043 · VCV1729755

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.005%, amr)

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 0.9	GERP -1.6, phastCons 1
Overall
CADD	11.66	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.005% Admixed American · 3/59,994 alleles

Filtering AF 0.00133% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000668%

Overall 0.000248% 4/1,613,958 alleles · very rare exomes 3/1,461,780 · genomes 1/152,178 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.005%	19,998
South Asian	0.0011%	91,088

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.Ser1111=
Coding: c.3333C>T
MANE Select: NM_001166108
dbSNP: rs1762303043
Type: single nucleotide variant
Location: chr4:168925053 (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-ser1111 (accessed [today's date]).

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