# NM_052844.4(DYNC2I2):c.65C>T (p.Ala22Val)

https://sugi.bio/variant/dync2i2-p-ala22val

## Summary

**DYNC2I2 p.Ala22Val (c.65C>T)** is classified **Benign/Likely benign** in DYNC2I2 (ClinVar, Multiple submitters, 7 submitters; last evaluated 2026-01-26). AlphaMissense: likely benign (0.2015); Low-frequency (popmax 1.33%, mid); Associated with short-rib thoracic dysplasia 11 with or without polydactyly.

**At a glance:** Benign/Likely benign · review: Multiple submitters · rsID rs201715229 · 7 submitters · 1 linked condition · AlphaMissense likely benign · low-frequency (popmax 1.33%, mid)

## For patients & families {#patients}

This is a change in the DYNC2I2 gene that is classified as benign/likely benign — not considered disease-causing, submitted by 7 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.Ala22Val |
| Coding change (HGVS c.) | c.65C>T |
| MANE Select transcript | [NM_052844](https://www.ncbi.nlm.nih.gov/nuccore/NM_052844) |
| dbSNP | [rs201715229](https://www.ncbi.nlm.nih.gov/snp/rs201715229/) |
| Variant type | single nucleotide variant |
| Location | chr9:128656662-128656662 (GRCh38) |
| ClinVar | [VCV931223](https://www.ncbi.nlm.nih.gov/clinvar/variation/931223/) |

**All HGVS expressions:** `NC_000009.11:g.131418941G>A`, `NC_000009.12:g.128656662G>A`, `NG_034056.1:g.5189C>T`, `NM_052844.4:c.65C>T`

## Computational & population evidence {#evidence}

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

- AlphaMissense **likely benign** (0.2015)
- REVEL 0.256 (benign-leaning) — agrees with AlphaMissense
- SaProt LLR -7.206 (tolerated) — agrees with AlphaMissense
- → **In-silico consensus:** AlphaMissense, REVEL and SaProt all call this tolerated
- SpliceAI predicts **donor gain** (Δ 0.21) — a splice-altering prediction the current classification does not reflect
- Conservation: phyloP 8.784, GERP 1.27, phastCons 1 — highly conserved (differs from AlphaMissense)
- CADD: **PHRED 23.6**. 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.*
- Regional missense constraint: **o/e 1.02** across the covering region of the MANE Select transcript (128,633,747–128,656,726), spanning 22,979 bp. Chi-square p 0.59. Describes the region, not this allele; gnomAD v4.1.1's own constrained determination. *Descriptive; no ACMG code applied.*
- SpliceAI deltas (raw): acceptor loss **0.00**, donor loss **0.00**, acceptor gain **0.00**, donor gain **0.21**. Largest is donor gain.
- SpliceAI deltas (masked): acceptor loss **0.00**, donor loss **0.00**, acceptor gain **0.00**, donor gain **0.21**.
- Population frequency (gnomAD v4.1): grpmax **1.33%** (mid) · FAF95 1.07% · FAF99 0.974% · 65/4,902 in the highest group · 4,754/1,509,876 alleles overall — low-frequency (popmax 1.33%, mid).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| Ashkenazi Jewish (not grpmax-eligible) | 2.17% | 46 |
| Middle Eastern (grpmax) | 1.33% | 75 |
| Remaining individuals (not grpmax-eligible) | 0.464% | 216 |
| Amish (not grpmax-eligible) | 0.439% | 228 |
| Admixed American | 0.31% | 322 |
| South Asian | 0.297% | 336 |
| European (non-Finnish) | 0.297% | 337 |
| Finnish (not grpmax-eligible) | 0.074% | 1,351 |
| African / African-American | 0.0503% | 1,987 |

Ashkenazi Jewish 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}

Residue **22** lies in a UniProt-annotated variant site (in).

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/Likely benign** — review status Multiple submitters *(criteria provided, multiple submitters, no conflicts)*, last evaluated 2026-01-26.

**Submitter consensus:** conflicting (5 Benign, 1 Likely benign).

**Submission history:** 7 submissions (2018–2026); classifications have differed over time.

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Centre for Mendelian Genomics, University Medical Centre Ljubljana | Benign | criteria provided, single submitter | clinical testing | 2018-10-29 |
| GeneDx | Benign | criteria provided, single submitter | clinical testing | 2019-09-20 |
| Breakthrough Genomics, Breakthrough Genomics | Benign | criteria provided, single submitter | not provided |  |
| PreventionGenetics, part of Exact Sciences | Benign | no assertion criteria provided | clinical testing | 2019-03-26 |
| Dr. Peter K. Rogan Lab, Western University |  | no classification provided | in vitro |  |
| Labcorp Genetics (formerly Invitae), Labcorp | Benign | criteria provided, single submitter | clinical testing | 2026-01-26 |
| CeGaT Center for Human Genetics Tuebingen | Likely benign | criteria provided, single submitter | clinical testing | 2025-09-01 |

## 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, See cases, not provided, DYNC2I2-related disorder, Ovarian serous cystadenocarcinoma, DYNC2I2-related condition, none provided, SHORT-RIB THORACIC DYSPLASIA 11 WITHOUT POLYDACTYLY.

## Same-residue context {#hotspot}

Residue **22** carries **1 other pathogenic ClinVar variant** — a recurrently-mutated position: [DYNC2I2 p.Ala22fs](/variant/dync2i2-p-ala22fs). *Positional co-occurrence of independent ClinVar records, not functional proof.*

## Similar variants {#similar}

Related DYNC2I2 variant pages (same residue, condition, or type): [DYNC2I2 p.Ala22fs](/variant/dync2i2-p-ala22fs), [SET p.Leu22=](/variant/set-p-leu22), [SET p.Leu22Pro](/variant/set-p-leu22pro), [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).

### Data sources & attribution {#sources}

ClinVar (NCBI — public domain, built 2026-10-14); 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 2026-10-14); 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 931223). 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.*