# NM_203486.3(DLL3):c.933G>A (p.Val311=)

https://sugi.bio/variant/dll3-p-val311

## Summary

**DLL3 p.Val311= (c.933G>A)** is classified **Conflicting classifications of pathogenicity** in DLL3 (ClinVar, Conflicting submitters, 2 submitters; last evaluated 2022-05-10). Very rare (popmax 0.00102%, nfe); Associated with spondylocostal dysostosis 1, autosomal recessive.

**At a glance:** Conflicting classifications of pathogenicity · review: Conflicting submitters · rsID rs760420806 · 2 submitters · 2 linked conditions · very rare (popmax 0.00102%, nfe)

## For patients & families {#patients}

This is a change in the DLL3 gene that is of uncertain or conflicting significance (submitters disagree on it), submitted by 2 submitters, and is linked to spondylocostal dysostosis 1, autosomal recessive.

*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:** [Condition overview & support (NIH GARD)](https://rarediseases.info.nih.gov/diseases/0010726/index) · [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [DLL3](https://sugi.bio/atlas/gene/DLL3/) |
| Protein change (HGVS p.) | p.Val311= |
| Coding change (HGVS c.) | c.933G>A |
| MANE Select transcript | [NM_203486](https://www.ncbi.nlm.nih.gov/nuccore/NM_203486) |
| dbSNP | [rs760420806](https://www.ncbi.nlm.nih.gov/snp/rs760420806/) |
| Variant type | single nucleotide variant |
| Location | chr19:39505291-39505291 (GRCh38) |
| ClinVar | [VCV894587](https://www.ncbi.nlm.nih.gov/clinvar/variation/894587/) |

**All HGVS expressions:** `NC_000019.10:g.39505291G>A`, `NC_000019.9:g.39995931G>A`, `NG_008256.1:g.11375G>A`, `NM_016941.4:c.933G>A`, `NM_203486.3:c.933G>A`

## 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 and, for splice-region changes, SpliceAI (below), not from a missing predictor score.
- SpliceAI predicts **donor gain** (Δ 0.35) — a splice-altering prediction the current classification does not reflect
- Conservation: phyloP 6.877, GERP -3.69, phastCons 1 — highly conserved position (PP3-type support)
- CADD: **PHRED 17.94**. 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 deltas (raw): acceptor loss **0.00**, donor loss **0.00**, acceptor gain **0.02**, donor gain **0.35**. Largest is donor gain.
- SpliceAI deltas (masked): acceptor loss **0.00**, donor loss **0.00**, acceptor gain **0.02**, donor gain **0.35**.
- Population frequency (gnomAD v4.1): grpmax **0.00102%** (nfe) · FAF95 0.000542% · FAF99 0.000428% · 12/1,180,046 in the highest group · 13/1,614,090 alleles overall — very rare (popmax 0.00102%, nfe).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| Remaining individuals (not grpmax-eligible) | 0.0016% | 62,488 |
| European (non-Finnish) (grpmax) | 0.00102% | 98,337 |

Remaining individuals shows a higher raw frequency than the grpmax group. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and "Remaining individuals" — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

*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}

**DLL3** population constraint: LOEUF 1.512, pLI 3.0199e-20, missense-Z -3.403. *Lower LOEUF and higher pLI indicate a gene that tolerates loss-of-function poorly; ClinGen dosage is the curated haploinsufficiency call.*

## Protein context {#protein}


AlphaFold model confidence (whole protein): pLDDT 65.42, 7% of residues very-high.

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

*Describes the biological roles of DLL3 (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.*


### Pathways affected {#pathways}

DLL3 participates in **2 Reactome pathways** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| [Formation of paraxial mesoderm](https://reactome.org/content/detail/R-HSA-9793380) | other |
| [Somitogenesis](https://reactome.org/content/detail/R-HSA-9824272) | other |

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

**Biological process:** skeletal system development.

## Clinical significance {#significance}

**Conflicting classifications of pathogenicity** — review status Conflicting submitters *(criteria provided, conflicting classifications)*, last evaluated 2022-05-10.

**Submitter consensus:** conflicting (2 Uncertain significance, 1 Likely benign).

**Submission history:** 3 submissions (2018–2022); classifications have differed over time.

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Illumina Laboratory Services, Illumina | Uncertain significance | criteria provided, single submitter | clinical testing | 2018-01-13 |
| Labcorp Genetics (formerly Invitae), Labcorp | Likely benign | criteria provided, single submitter | clinical testing | 2022-05-10 |

## Associated conditions {#conditions}

[spondylocostal dysostosis 1, autosomal recessive](https://sugi.bio/atlas/disease/spondylocostal-dysostosis-1-autosomal-recessive/), [syndactyly](https://sugi.bio/atlas/disease/syndactyly/).

**Reported phenotype names (ClinVar):** Spondylocostal dysostosis 1, autosomal recessive, Syndactyly, not provided, DLL3-Related Spondylocostal Dysostosis, Autosomal Recessive, none provided, Webbed fingers or toes.

## Similar variants {#similar}

Related DLL3 variant pages (same residue, condition, or type): [DLL3 c.652+1G>T](/variant/dll3-c-652-plus-1g-t), [DLL3 p.Arg238Ter](/variant/dll3-p-arg238ter), [DLL3 p.Cys178Ter](/variant/dll3-p-cys178ter), [DLL3 p.Cys207Ter](/variant/dll3-p-cys207ter), [DLL3 p.Cys379Tyr](/variant/dll3-p-cys379tyr), [DLL3 p.Gln346Ter](/variant/dll3-p-gln346ter), [DLL3 p.Gly504Asp](/variant/dll3-p-gly504asp), [DLL3 c.1758+20C>G](/variant/dll3-c-1758-plus-20c-g).

### 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 894587). 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.*