# NM_052844.4(DYNC2I2):c.873C>T (p.Thr291=)

https://sugi.bio/variant/dync2i2-p-thr291

## Summary

**DYNC2I2 p.Thr291= (c.873C>T)** is classified **Benign** in DYNC2I2 (ClinVar, Multiple submitters, 5 submitters; last evaluated 2026-02-04). Common (popmax 88.7%, nfe) — too common for a highly-penetrant pathogenic allele; Associated with short-rib thoracic dysplasia 11 with or without polydactyly.

**At a glance:** Benign · review: Multiple submitters · rsID rs4837291 · 5 submitters · 1 linked condition · common (popmax 88.7%, nfe) — too common for a highly-penetrant pathogenic allele

## For patients & families {#patients}

This is a change in the DYNC2I2 gene that is classified as benign — not considered disease-causing, submitted by 5 submitters, and is linked to short-rib thoracic dysplasia 11 with or without polydactyly.

*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/0015996/index) · [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [DYNC2I2](https://sugi.bio/atlas/gene/DYNC2I2/) |
| Protein change (HGVS p.) | p.Thr291= |
| Coding change (HGVS c.) | c.873C>T |
| MANE Select transcript | [NM_052844](https://www.ncbi.nlm.nih.gov/nuccore/NM_052844) |
| dbSNP | [rs4837291](https://www.ncbi.nlm.nih.gov/snp/rs4837291/) |
| Variant type | single nucleotide variant |
| Location | chr9:128635200-128635200 (GRCh38) |
| ClinVar | [VCV516214](https://www.ncbi.nlm.nih.gov/clinvar/variation/516214/) |

**All HGVS expressions:** `NC_000009.11:g.131397479G>A`, `NC_000009.12:g.128635200G>A`, `NG_027748.1:g.87643G>A`, `NG_034056.1:g.26651C>T`, `NM_052844.4:c.873C>T`

## Computational & population evidence {#evidence}

**Concordance:** Evidence sources **disagree** — common (popmax 88.7%, nfe) — too common for a highly-penetrant pathogenic allele.

- **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 **acceptor gain** (Δ 0.69) — a splice-altering prediction the current classification does not reflect
- Conservation: phyloP -15.955, GERP -2.73 — fast-evolving / accelerated position
- CADD: **PHRED 0.009**. 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 **0.05**, donor loss **0.00**, acceptor gain **0.69**, donor gain **0.00**. Largest is acceptor gain.
- SpliceAI deltas (masked): acceptor loss **0.00**, donor loss **0.00**, acceptor gain **0.69**, donor gain **0.00**.
- Pangolin: Δ**0.48** (gain), gain 0.48 / loss 0.00. Agrees with SpliceAI. An independent predictor to SpliceAI — a different model trained on different data. *Descriptive; ClinGen's SVI calibration covers SpliceAI, not Pangolin, so no ACMG code is assigned.*
- Population frequency (gnomAD v4.1): grpmax **88.7%** (nfe) · FAF95 88.6% · FAF99 88.5% · 1,046,648/1,179,926 in the highest group · 1,351,091/1,613,070 alleles overall — common (popmax 88.7%, nfe) — too common for a highly-penetrant pathogenic allele.

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| Amish (not grpmax-eligible) | 95.3% | 1 |
| European (non-Finnish) (grpmax) | 88.7% | 1 |
| Ashkenazi Jewish (not grpmax-eligible) | 88.7% | 1 |
| Finnish (not grpmax-eligible) | 82.4% | 1 |
| Middle Eastern | 82.3% | 1 |
| Remaining individuals (not grpmax-eligible) | 81.8% | 1 |
| Admixed American | 78.5% | 1 |
| South Asian | 77.2% | 1 |
| East Asian | 47.2% | 2 |
| African / African-American | 40.8% | 2 |

Amish 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}

**DYNC2I2** population constraint: LOEUF 1.036, pLI 8.6153e-12, missense-Z -0.55611. *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):

- **short-rib thoracic dysplasia 11 with or without polydactyly** — Definitive (AR)

## Protein context {#protein}


AlphaFold model confidence (whole protein): pLDDT 82.66, 65% of residues very-high.

**4 experimental structure(s)** (PDB): [6RLB](https://www.rcsb.org/structure/6RLB), [6SC2](https://www.rcsb.org/structure/6SC2), [8RGG](https://www.rcsb.org/structure/8RGG), [8RGH](https://www.rcsb.org/structure/8RGH).

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

*Describes the biological roles of DYNC2I2 (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:** DYNC2I2's established molecular role includes dynein light chain binding.


### Pathways affected {#pathways}

DYNC2I2 participates in **1 Reactome pathway** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| [Intraflagellar transport](https://reactome.org/content/detail/R-HSA-5620924) | curated |

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

**Molecular function:** dynein light chain binding.

**Biological process:** intraciliary retrograde transport, cilium assembly.

## Clinical significance {#significance}

**Benign** — review status Multiple submitters *(criteria provided, multiple submitters, no conflicts)*, last evaluated 2026-02-04.

**Submitter consensus:** unanimous (5/5 Benign).

**Submission history:** 5 submissions (2017–2026); classifications have been stable.

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| GeneDx | Benign | criteria provided, single submitter | clinical testing | 2017-10-26 |
| Genome-Nilou Lab | Benign | criteria provided, single submitter | clinical testing | 2021-12-05 |
| Breakthrough Genomics, Breakthrough Genomics | Benign | criteria provided, single submitter | not provided |  |
| Labcorp Genetics (formerly Invitae), Labcorp | Benign | criteria provided, single submitter | clinical testing | 2026-02-04 |
| Blueprint Genetics | Benign | criteria provided, single submitter | clinical testing | 2024-11-27 |

## Associated conditions {#conditions}

[short-rib thoracic dysplasia 11 with or without polydactyly](https://sugi.bio/atlas/disease/short-rib-thoracic-dysplasia-11-with-or-without-polydactyly/).

**Reported phenotype names (ClinVar):** Short-rib thoracic dysplasia 11 with or without polydactyly, not specified, not provided, AllHighlyPenetrant, SHORT-RIB THORACIC DYSPLASIA 11 WITHOUT POLYDACTYLY, none provided.

## Similar variants {#similar}

Related DYNC2I2 variant pages (same residue, condition, or type): [DYNC2I2 p.Thr291del](/variant/dync2i2-p-thr291del), [DYNC2I2 c.1372+1G>A](/variant/dync2i2-c-1372-plus-1g-a), [DYNC2I2 p.Arg121Ter](/variant/dync2i2-p-arg121ter), [DYNC2I2 p.Arg182Trp](/variant/dync2i2-p-arg182trp), [DYNC2I2 p.Arg447Trp](/variant/dync2i2-p-arg447trp), [DYNC2I2 p.Ala131Val](/variant/dync2i2-p-ala131val), [DYNC2I2 p.Ala13Gly](/variant/dync2i2-p-ala13gly), [DYNC2I2 p.Ala219Thr](/variant/dync2i2-p-ala219thr).

### Data sources & attribution {#sources}

ClinVar (NCBI — public domain, built 2026-10-14); gnomAD v4.1 (Broad Institute, built 2026-10-14); 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 2026-10-14); 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 516214). 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.*