Is CD19 p.Ser437= (c.1311C>T) pathogenic?

CD19 p.Ser437= (c.1311C>T) is classified Benign/Likely benign in CD19 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2026-01-24). Rare (popmax 0.974%, afr); Associated with immunodeficiency, common variable, 3.

What condition is associated with CD19 p.Ser437= (c.1311C>T)?

CD19 p.Ser437= (c.1311C>T) is associated with immunodeficiency, common variable, 3 (ClinVar).

How common is CD19 p.Ser437= (c.1311C>T) in the general population?

CD19 p.Ser437= (c.1311C>T) is rare (popmax 0.974%, afr) (gnomAD).

CD19 p.Ser437=

c.1311C>T · rs148047850 · VCV318809

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

rare (popmax 0.974%, afr)

Conditions

immunodeficiency, common variable, 3

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 -2.2
Overall
CADD	7.827	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.974% African / African-American · 731/75,024 alleles

Filtering AF 0.916% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.892%

Overall 0.0537% 867/1,614,112 alleles · rare exomes 430/1,461,850 · genomes 437/152,262 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.974%	103
Admixed American	0.0916%	1,091
Remaining individualsnot grpmax-eligible	0.0896%	1,116
Middle Eastern	0.0825%	1,212
South Asian	0.00549%	18,218
East Asian	0.00223%	44,880
European (non-Finnish)	0.00119%	84,285

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: CD19
Protein: p.Ser437=
Coding: c.1311C>T
MANE Select: NM_001770
dbSNP: rs148047850
Type: single nucleotide variant
Location: chr16:28937462 (GRCh38)
Gene constraint: LOEUF 0.627 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 62.99 · 4 PDB
Residue 437: the 'disordered' region

Full CD19 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

immunodeficiency, common variable, 3 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CD19 c.835+3A>G Uncertain significance ★★ same condition
CD19 p.Arg163His Uncertain significance ★★ ⚠ same condition
CD19 p.Arg263His Uncertain significance ★★ ⚠ same condition
CD19 p.Arg490Gln Uncertain significance ★★ ⚠ same condition
CD19 p.Arg76Ser Uncertain significance ★★ ⚠ same condition
CD19 p.Gln345His Uncertain significance ★★ ⚠ same condition
CD19 p.Glu21Gln Uncertain significance ★★ ⚠ same condition
CD19 p.Glu29Gln 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/cd19-p-ser437 (accessed [today's date]).

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