# NM_001370465.2(DUSP28):c.38C>T (p.Ser13Leu)

https://sugi.bio/variant/dusp28-p-ser13leu

## Summary

**DUSP28 p.Ser13Leu (c.38C>T)** is classified **Uncertain significance** in DUSP28 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-12-27). AlphaMissense: likely benign (0.1397); Ultra-rare (popmax 0.0221%, nfe).

**At a glance:** Uncertain significance · review: Single submitter · rsID rs778568184 · 1 submitter · AlphaMissense likely benign · ultra-rare (popmax 0.0221%, nfe)

## For patients & families {#patients}

This is a change in the DUSP28 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 | [DUSP28](https://sugi.bio/atlas/gene/DUSP28/) |
| Protein change (HGVS p.) | p.Ser13Leu |
| Coding change (HGVS c.) | c.38C>T |
| MANE Select transcript | [NM_001282771](https://www.ncbi.nlm.nih.gov/nuccore/NM_001282771) (variant reported on NM_001370465) |
| dbSNP | [rs778568184](https://www.ncbi.nlm.nih.gov/snp/rs778568184/) |
| Variant type | single nucleotide variant |
| Location | chr2:240560722-240560722 (GRCh38) |
| ClinVar | [VCV2386645](https://www.ncbi.nlm.nih.gov/clinvar/variation/2386645/) |

**All HGVS expressions:** `NC_000002.11:g.241500139C>T`, `NC_000002.12:g.240560722C>T`, `NG_168984.1:g.27C>T`, `NM_001033575.1:c.38C>T`, `NM_001308375.4:c.220+9G>A`, `NM_001354023.3:c.-334+9G>A`, `NM_001354024.3:c.-122+9G>A`, `NM_001354026.3:c.-122+9G>A`, `NM_001370465.2:c.38C>T`, `NM_001393462.1:c.-255+9G>A`, `NM_001393463.1:c.-122+9G>A`, `NM_001393464.1:c.5+314G>A`, `NM_001393465.1:c.-122+9G>A`, `NM_001393466.1:c.-18+9G>A`, `NM_001393467.1:c.-122+9G>A`, `NM_001393468.1:c.-122+9G>A`, `NM_001393469.1:c.-122+9G>A`, `NM_001393470.1:c.-122+9G>A`, `NM_001393471.1:c.5+314G>A`, `NM_001393472.1:c.-122+9G>A`, `NM_001393474.1:c.-122+9G>A`, `NM_001393475.1:c.-255+9G>A`, `NM_001393476.1:c.-91+9G>A`, `NM_001393477.1:c.-122+9G>A`, `NM_001393478.1:c.-91+9G>A`, `NM_001393479.1:c.-334+9G>A`, `NM_001393481.1:c.5+314G>A`, `NM_001393482.1:c.-52+9G>A`, `NM_001393483.1:c.-122+9G>A`, `NM_001393484.1:c.-91+9G>A`, `NM_001393485.1:c.-564+9G>A`

## Computational & population evidence {#evidence}

**Concordance:** ClinVar classifies this **uncertain**; the computational predictors unanimously lean **tolerated** — a triage signal, not a reclassification.

- AlphaMissense **likely benign** (0.1397)
- REVEL 0.039 (moderately benign-leaning) — agrees with AlphaMissense
- SaProt LLR -6.543 (tolerated) — agrees with AlphaMissense
- → **In-silico consensus:** AlphaMissense, REVEL and SaProt all call this tolerated
- Conservation: phyloP -0.734, GERP -1.93 — not a conserved position (phyloP < 0.1, ACGS BP7 cut)
- CADD: **PHRED 0.165**. 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 1.38** across the covering region of the MANE Select transcript (240,560,685–240,561,464), spanning 779 bp. Chi-square p 4.4e-10. Describes the region, not this allele; gnomAD v4.1.1's own constrained determination. *Descriptive; no ACMG code applied.*
- SpliceAI: **not looked up on this page** — it was served without the gene's SpliceAI index, so no lookup was made. This is a gap in this page, not in the data, and says nothing about whether a splicing effect is predicted.
- Population frequency (gnomAD v4.1): grpmax **0.0221%** (nfe) · FAF95 0.0199% · FAF99 0.0189% · 254/1,148,230 in the highest group · 262/1,524,812 alleles overall — ultra-rare (popmax 0.0221%, nfe).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| European (non-Finnish) (grpmax) | 0.0221% | 4,521 |
| Remaining individuals (not grpmax-eligible) | 0.0068% | 14,699 |
| African / African-American | 0.00431% | 23,215 |
| Admixed American | 0.00208% | 47,996 |

*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.*

## Clinical significance {#significance}

**Uncertain significance** — review status Single submitter *(criteria provided, single submitter)*, last evaluated 2022-12-27.

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

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Ambry Genetics | Uncertain significance | criteria provided, single submitter | clinical testing | 2022-12-27 |

**Reported phenotype names (ClinVar):** not specified, AllHighlyPenetrant.

### 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 2386645). 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.*