# NM_001261413.2(DCTN2):c.503A>T (p.Asp168Val)

https://sugi.bio/variant/dctn2-p-asp168val

## Summary

**DCTN2 p.Asp168Val (c.503A>T)** is classified **Uncertain significance** in DCTN2 (ClinVar, Single submitter, 1 submitter). AlphaMissense: likely pathogenic (0.822); Absent from gnomAD v4.1.

**At a glance:** Uncertain significance · review: Single submitter · rsID rs2140121175 · 1 submitter · AlphaMissense likely pathogenic · absent from gnomAD v4.1

## For patients & families {#patients}

This is a change in the DCTN2 gene that is currently of uncertain significance — a definitive interpretation has not yet been established, 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 | [DCTN2](https://sugi.bio/atlas/gene/DCTN2/) |
| Protein change (HGVS p.) | p.Asp168Val |
| Coding change (HGVS c.) | c.503A>T |
| MANE Select transcript | [NM_001261413](https://www.ncbi.nlm.nih.gov/nuccore/NM_001261413) |
| dbSNP | [rs2140121175](https://www.ncbi.nlm.nih.gov/snp/rs2140121175/) |
| Variant type | single nucleotide variant |
| Location | chr12:57534313-57534313 (GRCh38) |
| ClinVar | [VCV1330219](https://www.ncbi.nlm.nih.gov/clinvar/variation/1330219/) |

**All HGVS expressions:** `NC_000012.11:g.57928096T>A`, `NC_000012.12:g.57534313T>A`, `NG_047120.1:g.18019A>T`, `NM_001261412.2:c.509A>T`, `NM_001261413.2:c.503A>T`, `NM_001348065.2:c.638A>T`, `NM_001348066.2:c.434A>T`, `NM_001348067.2:c.242A>T`, `NM_001348068.2:c.242A>T`, `NM_006400.5:c.518A>T`, `NR_145419.2:n.638A>T`

## Computational & population evidence {#evidence}

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

- AlphaMissense **likely pathogenic** (0.822)
- REVEL 0.889 (moderately pathogenic-leaning) — agrees with AlphaMissense
- SaProt LLR -9.481 (tolerated) — differs from AlphaMissense
- → **In-silico consensus:** AlphaMissense and REVEL call this damaging; SaProt does not
- Conservation: phyloP 7.879, GERP 2.35, phastCons 1 — highly conserved (agrees)
- CADD: **PHRED 27.1**. 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 0.90** across the covering region of the MANE Select transcript (57,530,692–57,534,343), spanning 3,651 bp. Chi-square p 0.083. Describes the region, not this allele; gnomAD v4.1.1's own constrained determination. *Descriptive; no ACMG code 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: **absent from gnomAD v4.1** — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

*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}

**DCTN2** population constraint: LOEUF 0.54, pLI 0.87043, missense-Z 1.4422. *Lower LOEUF and higher pLI indicate a gene that tolerates loss-of-function poorly; ClinGen dosage is the curated haploinsufficiency call.*

## Protein context {#protein}

Residue **168** lies in an α-helix.

AlphaFold model confidence (whole protein): pLDDT 77.22, 27% of residues very-high.

**2 experimental structure(s)** (PDB): [9B7J](https://www.rcsb.org/structure/9B7J), [9B85](https://www.rcsb.org/structure/9B85).

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

*Describes the biological roles of DCTN2 (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:** DCTN2's established molecular role includes protein kinase binding.


### Pathways affected {#pathways}

DCTN2 participates in **12 Reactome pathways** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| [Processing of antigen in germinal center B cells](https://reactome.org/content/detail/R-HSA-9979719) | curated |
| [AURKA Activation by TPX2](https://reactome.org/content/detail/R-HSA-8854518) | other |
| [Anchoring of the basal body to the plasma membrane](https://reactome.org/content/detail/R-HSA-5620912) | other |
| [COPI-independent Golgi-to-ER retrograde traffic](https://reactome.org/content/detail/R-HSA-6811436) | other |
| [COPI-mediated anterograde transport](https://reactome.org/content/detail/R-HSA-6807878) | other |
| [HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand](https://reactome.org/content/detail/R-HSA-3371497) | other |
| [Loss of Nlp from mitotic centrosomes](https://reactome.org/content/detail/R-HSA-380259) | other |
| [Loss of proteins required for interphase microtubule organization from the centrosome](https://reactome.org/content/detail/R-HSA-380284) | other |
| [MHC class II antigen presentation](https://reactome.org/content/detail/R-HSA-2132295) | other |
| [Recruitment of NuMA to mitotic centrosomes](https://reactome.org/content/detail/R-HSA-380320) | other |
| [Recruitment of mitotic centrosome proteins and complexes](https://reactome.org/content/detail/R-HSA-380270) | other |
| [Regulation of PLK1 Activity at G2/M Transition](https://reactome.org/content/detail/R-HSA-2565942) | other |

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

**Molecular function:** protein kinase binding, spectrin binding, identical protein binding.

**Biological process:** mitotic spindle organization, mitotic metaphase chromosome alignment, protein localization to centrosome.

## Clinical significance {#significance}

**Uncertain significance** — review status Single submitter *(criteria provided, single submitter)*.

**Submitter consensus:** unanimous (1/1 Uncertain significance).

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences | Uncertain significance | criteria provided, single submitter | clinical testing |  |

**Reported phenotype names (ClinVar):** See cases.

## Similar variants {#similar}

Related DCTN2 variant pages (same residue, condition, or type): [DCTN2 c.1119+7G>A](/variant/dctn2-c-1119-plus-7g-a), [DCTN2 p.Ala162Gly](/variant/dctn2-p-ala162gly), [DCTN2 p.Ala7Ser](/variant/dctn2-p-ala7ser), [DCTN2 p.Arg332Ile](/variant/dctn2-p-arg332ile), [DCTN2 p.Arg379Cys](/variant/dctn2-p-arg379cys), [DCTN2 p.Arg395Gln](/variant/dctn2-p-arg395gln), [DCTN2 p.Asp216Asn](/variant/dctn2-p-asp216asn), [DCTN2 p.Asp216Glu](/variant/dctn2-p-asp216glu).

### 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 1330219). 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.*