Is PACS2 p.Val20= (c.60G>A) pathogenic?

PACS2 p.Val20= (c.60G>A) is classified Likely benign in PACS2 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-09-01). Very rare (popmax 0.0016%, afr).

How common is PACS2 p.Val20= (c.60G>A) in the general population?

PACS2 p.Val20= (c.60G>A) is very rare (popmax 0.0016%, afr) (gnomAD).

PACS2 p.Val20=

c.60G>A · rs893256021 · VCV2056588

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.0016%, afr)

⚠ 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 6.8	GERP 1.2, phastCons 1
Overall
CADD	15.73	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0016% African / African-American · 1/62,356 alleles

Overall 8.02e-05% 1/1,246,256 alleles · very rare exomes 0/1,097,880 · genomes 1/148,376 · 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: PACS2
Protein: p.Val20=
Coding: c.60G>A
MANE Select: NM_001100913
dbSNP: rs893256021
Type: single nucleotide variant
Location: chr14:105314978 (GRCh38)

Full PACS2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

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/pacs2-p-val20 (accessed [today's date]).

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