Is PALLD p.Ser582= (c.1746T>A) pathogenic?

PALLD p.Ser582= (c.1746T>A) is classified Likely benign in PALLD (ClinVar, Single submitter, 1 submitter; last evaluated 2021-10-25). Absent from gnomAD v4.1.

How common is PALLD p.Ser582= (c.1746T>A) in the general population?

PALLD p.Ser582= (c.1746T>A) is absent from gnomAD v4.1 (gnomAD).

PALLD p.Ser582=

c.1746T>A · rs1206394162 · VCV1779304

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.89	GERP -3.1
Overall
CADD	1.935	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: PALLD
Protein: p.Ser582=
Coding: c.1746T>A
MANE Select: NM_001166108
dbSNP: rs1206394162
Type: single nucleotide variant
Location: chr4:168711705 (GRCh38)
Gene constraint: LOEUF 0.644 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 54.74 · 2 PDB

Full PALLD gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

PALLD p.Ser582Pro Uncertain significance ★ same residue
PALLD p.Ser582Thr Uncertain significance ★ same residue
PALLD c.1965-12532C>A Uncertain significance ★★ same type
PALLD c.1965-12532C>G Uncertain significance ★★ same type
PALLD c.1965-12534C>A Uncertain significance ★★ same type
PALLD c.1965-12535A>C Uncertain significance ★★ same type
PALLD c.1965-12544A>G Uncertain significance ★★ same type
PALLD c.1965-12549T>C Uncertain significance ★★ same type

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-ser582 (accessed [today's date]).

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