# NM_001770.6(CD19):c.286C>T (p.Leu96=)

https://sugi.bio/variant/cd19-p-leu96

## Summary

**CD19 p.Leu96= (c.286C>T)** is classified **Likely benign** in CD19 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-07-01). Very rare (popmax 0.000137%).

**At a glance:** Likely benign · review: Single submitter · rsID rs751791834 · 1 submitter · very rare (popmax 0.000137%)

## For patients & families {#patients}

This is a change in the CD19 gene that is classified as likely benign — not considered disease-causing, submitted by 1 submitter.

*Reference information, not medical advice, and not a prediction for any individual. A genetic counselor or clinician can interpret what it means for you and your family.*

**Support & next steps:** [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [CD19](https://sugi.bio/atlas/gene/CD19/) |
| Protein change (HGVS p.) | p.Leu96= |
| Coding change (HGVS c.) | c.286C>T |
| MANE Select transcript | [NM_001770](https://www.ncbi.nlm.nih.gov/nuccore/NM_001770) |
| dbSNP | [rs751791834](https://www.ncbi.nlm.nih.gov/snp/rs751791834/) |
| Variant type | single nucleotide variant |
| Location | chr16:28932543-28932543 (GRCh38) |
| ClinVar | [VCV1128108](https://www.ncbi.nlm.nih.gov/clinvar/variation/1128108/) |

**All HGVS expressions:** `LRG_35:g.5605C>T`, `NC_000016.10:g.28932543C>T`, `NC_000016.9:g.28943864C>T`, `NG_007275.1:g.5605C>T`, `NM_001178098.2:c.286C>T`, `NM_001385732.1:c.89-368C>T`, `NM_001770.6:c.286C>T`, `NR_169755.1:n.316C>T`

## Computational & population evidence {#evidence}

**Concordance:** Mixed / partial computational evidence (see below).

- **Missense predictors (AlphaMissense/REVEL/SaProt) do not apply** to this variant type — they score amino-acid substitutions only. For non-missense variants the computational signal comes from conservation (below), not from a missing predictor score.
- Conservation: phyloP -0.507, phastCons 0.026 — not a conserved position (phyloP < 0.1, ACGS BP7 cut)
- CADD: **PHRED 5.073**. No single ClinGen-calibrated threshold exists and the expert panels that use CADD disagree — GUCY2D/AIPL1 require ≥ 20.0 for an untranslated-region variant, ABCA4 ≥ 28.1 for a synonymous or indel variant, the Pulmonary Hypertension panel imports Pejaver 2022's missense-calibrated numbers, and the Antibody Deficiencies panel declines CADD entirely for PIK3CD. CADD v1.7 also incorporates Zoonomia phyloP, so it partly re-expresses the conservation above. *Descriptive; no threshold applied.*
- SpliceAI: **not assessed** — no allele at this position is in our SpliceAI release, either because it lies outside the scored MANE transcript scope or because every allele is below Δ0.2. We cannot tell which, so this claims neither; absence is not evidence against a splicing effect.
- Population frequency (gnomAD v4.1): global (via dbSNP) **0.000137%** · 2/1,461,580 alleles overall — very rare (popmax 0.000137%).

*Computational predictors are not independent (ClinGen Variant Classification guidance): AlphaMissense (Cheng et al. 2023) carries the ACMG weight for missense and conservation (phyloP/GERP/phastCons) for non-missense; REVEL (Pejaver-2022 calibrated strength bands) and SaProt (Su et al. 2023, structure-aware, ClinVar-independent protein language model, raw LLR) are shown as orthogonal agreement signals, not additive. For frequency, the gnomAD v4.1 grpmax filtering allele frequency (FAF95) is ClinGen's designated BA1/BS1 input (gnomAD v4 guidance v3.0, June 2025); BA1/BS1 thresholds are disease-specific, not a blanket 5%. Predictions, not a clinical determination.*

## Gene constraint & dosage {#gene-context}

**CD19** population constraint: LOEUF 0.627, pLI 0.0059088, missense-Z 1.3202; ClinGen dosage — haploinsufficiency 30, triplosensitivity 0 (0–3 scale). *Lower LOEUF and higher pLI indicate a gene that tolerates loss-of-function poorly; ClinGen dosage is the curated haploinsufficiency call.*

Curated gene–disease validity (ClinGen):

- **immunodeficiency, common variable, 3** — Definitive (AR)

## Protein context {#protein}

Residue **96** lies in a disulfide bond; the ig-like c2-type 1 domain; a β-strand.

AlphaFold model confidence (whole protein): pLDDT 62.99, 24% of residues very-high.

**4 experimental structure(s)** (PDB): [6AL5](https://www.rcsb.org/structure/6AL5), [7JIC](https://www.rcsb.org/structure/7JIC), [7URV](https://www.rcsb.org/structure/7URV), [7URX](https://www.rcsb.org/structure/7URX) — incl. mutant structure 6AL5.

## What this gene does {#gene-function}

*Describes the biological roles of CD19 (the gene this variant disrupts) — not effects measured for this specific variant. A damaging variant is expected to affect these functions and pathways; the degree depends on the variant.*

**How this variant is thought to act:** p.Leu96= falls in the ig-like c2-type 1 domain. In Reactome, CD19 is annotated in disease pathway(s) including **Constitutive Signaling by Aberrant PI3K in Cancer**.

**Disease mechanism (Reactome):** CD19 loss or alteration is curated in [Constitutive Signaling by Aberrant PI3K in Cancer](https://reactome.org/content/detail/R-HSA-2219530).

### Pathways affected {#pathways}

CD19 participates in **6 Reactome pathways** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| ⚕ [Constitutive Signaling by Aberrant PI3K in Cancer](https://reactome.org/content/detail/R-HSA-2219530) | curated |
| [Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell](https://reactome.org/content/detail/R-HSA-198933) | curated |
| [PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling](https://reactome.org/content/detail/R-HSA-6811558) | curated |
| [PIP3 activates AKT signaling](https://reactome.org/content/detail/R-HSA-1257604) | curated |
| [Regulation of Complement cascade](https://reactome.org/content/detail/R-HSA-977606) | curated |
| [Antigen activates B Cell Receptor (BCR) leading to generation of second messengers](https://reactome.org/content/detail/R-HSA-983695) | electronic |

### Molecular function & processes (GO — experimentally supported) {#go}

**Biological process:** B cell proliferation involved in immune response, immunoglobulin mediated immune response, antigen receptor-mediated signaling pathway, regulation of B cell receptor signaling pathway, regulation of B cell activation, positive regulation of release of sequestered calcium ion into cytosol.

## Clinical significance {#significance}

**Likely benign** — review status Single submitter *(criteria provided, single submitter)*, last evaluated 2024-07-01.

**Submitter consensus:** unanimous (1/1 Likely benign).

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Labcorp Genetics (formerly Invitae), Labcorp | Likely benign | criteria provided, single submitter | clinical testing | 2024-07-01 |

**Reported phenotype names (ClinVar):** not provided, none provided.

## Similar variants {#similar}

Related CD19 variant pages (same residue, condition, or type): [CD19 p.Leu96Met](/variant/cd19-p-leu96met), [CD19 c.835+3A>G](/variant/cd19-c-835-plus-3a-g), [CD19 p.Ala191Thr](/variant/cd19-p-ala191thr), [CD19 p.Arg123Trp](/variant/cd19-p-arg123trp), [CD19 p.Arg163His](/variant/cd19-p-arg163his), [CD19 p.Arg234Cys](/variant/cd19-p-arg234cys), [CD19 p.Arg263His](/variant/cd19-p-arg263his), [CD19 p.Arg321Lys](/variant/cd19-p-arg321lys).

### Data sources & attribution {#sources}

ClinVar (NCBI — public domain, built 2026-10-11); gnomAD v4.1 (Broad Institute, built 2026-10-06); AlphaMissense (Cheng et al. 2023, © Google DeepMind — CC BY 4.0, built 2026-01-27); REVEL (Ioannidis et al. 2016 — ODbL, built 2026-07-13); SaProt (Su et al. 2023 — MIT, built 2026-07-14); SpliceAI (Illumina — free for non-commercial use, built 2026-10-13); CADD (Rentzsch et al. 2019, University of Washington — free for non-commercial use, built 2026-10-10); Conservation (phyloP/phastCons/GERP) (UCSC hg38 470-way mammal (Hiller Lab) + Ensembl Compara, built 2026-07-12); gnomAD Non-coding Constraint (Gnocchi) (Chen et al. 2024, Broad Institute — CC0, built 2026-10-11); gnomAD Regional Missense Constraint (Broad Institute — CC0, built 2026-10-13); Pangolin (Zeng & Li 2022 — CC BY 4.0, built 2026-10-11); Repeat regions (UCSC — RepeatMasker, TRF, segmental duplications, built 2026-10-11); ClinGen (ClinGen, built 2026-09-22); UniProt (CC BY 4.0); Reactome / GO (CC BY 4.0, built 2026-09-23); MaveDB (per-record license, built 2026-10-11); CIViC (CC0, built 2026-09-22); Orphanet (Orphanet, built 2026-06-12)

*Primary record: NCBI ClinVar (variation 1128108). Classifications reflect these databases as of the page's build date and may change. Free reference use — not medical advice; consult the primary submitters and a clinician.*