Is PAX5 p.Ser342= (c.1026C>T) pathogenic?

PAX5 p.Ser342= (c.1026C>T) is classified Likely benign in PAX5 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2024-11-17). Very rare (popmax 0.00833%, amr); Associated with Inborn genetic diseases.

What condition is associated with PAX5 p.Ser342= (c.1026C>T)?

PAX5 p.Ser342= (c.1026C>T) is associated with Inborn genetic diseases (ClinVar).

How common is PAX5 p.Ser342= (c.1026C>T) in the general population?

PAX5 p.Ser342= (c.1026C>T) is very rare (popmax 0.00833%, amr) (gnomAD).

PAX5 p.Ser342=

c.1026C>T · rs767690925 · VCV436161

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00833%, amr)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.454	indeterminate
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · G>T here scores Δ0.20 · evaluated, not missing
Constraint at this position
Conservation	phyloP -1.9	GERP -5.1
Overall
CADD	4.715	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00833% Admixed American · 5/59,998 alleles

Filtering AF 0.00323% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00236%

Overall 0.00384% 62/1,613,002 alleles · very rare exomes 55/1,460,788 · genomes 7/152,214 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00833%	12,000
African / African-American	0.00667%	14,985
Remaining individualsnot grpmax-eligible	0.00641%	15,605
South Asian	0.00439%	22,762
European (non-Finnish)	0.00356%	28,074
Finnishnot grpmax-eligible	0.00312%	32,012

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: PAX5
Protein: p.Ser342=
Coding: c.1026C>T
MANE Select: NM_016734
dbSNP: rs767690925
Type: single nucleotide variant
Location: chr9:36846916 (GRCh38)
Gene constraint: LOEUF 0.361 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
Structure: AlphaFold pLDDT 63.89 · 2 PDB

Full PAX5 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

PAX5 p.Ala308Thr Uncertain significance ★★ ⚠ same condition
PAX5 p.Ala383Val Uncertain significance ★★ ⚠ same condition
PAX5 p.Ala45Ser Uncertain significance ★★ ⚠ same condition
PAX5 p.Arg122Gln Uncertain significance ★★ ⚠ same condition
PAX5 p.Arg239Cys Uncertain significance ★★ ⚠ same condition
PAX5 p.Gln233Lys Uncertain significance ★★ ⚠ same condition
PAX5 p.Gly202Asp Uncertain significance ★★ ⚠ same condition
PAX5 p.Ile114Val Uncertain significance ★★ ⚠ same condition

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/pax5-p-ser342 (accessed [today's date]).

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