Is PALLD p.Ser972= (c.2916T>C) pathogenic?

PALLD p.Ser972= (c.2916T>C) is classified Likely benign in PALLD (ClinVar, Single submitter, 1 submitter; last evaluated 2020-08-10). Very rare (popmax 0.00136%, afr); Associated with pancreatic adenocarcinoma.

What condition is associated with PALLD p.Ser972= (c.2916T>C)?

PALLD p.Ser972= (c.2916T>C) is associated with pancreatic adenocarcinoma (ClinVar).

How common is PALLD p.Ser972= (c.2916T>C) in the general population?

PALLD p.Ser972= (c.2916T>C) is very rare (popmax 0.00136%, afr) (gnomAD).

PALLD p.Ser972=

c.2916T>C · rs566543059 · VCV1128788

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00136%, 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	0.347	indeterminate
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -6.7	GERP -4.7
Overall
CADD	6.194	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00136% African / African-American · 1/73,396 alleles

Overall 6.21e-05% 1/1,609,742 alleles · very rare exomes 0/1,461,524 · genomes 1/148,218 · joint denominator

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.Ser972=
Coding: c.2916T>C
MANE Select: NM_001166108
dbSNP: rs566543059
Type: single nucleotide variant
Location: chr4:168921599 (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-ser972 (accessed [today's date]).

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