Is PALLD p.Val1074= (c.3222G>C) pathogenic?

PALLD p.Val1074= (c.3222G>C) is classified Likely benign in PALLD (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-11-05). Ultra-rare (popmax 0.0254%, afr); Associated with pancreatic adenocarcinoma.

What condition is associated with PALLD p.Val1074= (c.3222G>C)?

PALLD p.Val1074= (c.3222G>C) is associated with pancreatic adenocarcinoma (ClinVar).

How common is PALLD p.Val1074= (c.3222G>C) in the general population?

PALLD p.Val1074= (c.3222G>C) is ultra-rare (popmax 0.0254%, afr) (gnomAD).

PALLD p.Val1074=

c.3222G>C · rs775271720 · VCV1728437

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0254%, 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	0.225	benign-leaning
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 1.8	GERP -1.8, phastCons 1
Overall
CADD	9.802	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0254% African / African-American · 19/74,922 alleles

Filtering AF 0.0166% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0137%

Overall 0.00118% 19/1,613,510 alleles · ultra-rare exomes 8/1,461,306 · genomes 11/152,204 · 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.Val1074=
Coding: c.3222G>C
MANE Select: NM_001166108
dbSNP: rs775271720
Type: single nucleotide variant
Location: chr4:168924418 (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-val1074 (accessed [today's date]).

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