# NM_145261.4(DNAJC19):c.3+16C>T

https://sugi.bio/variant/dnajc19-c-3-plus-16c-t

## Summary

**DNAJC19 c.3+16C>T** is classified **Likely benign** in DNAJC19 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2026-01-27). Ultra-rare (popmax 0.0196%, nfe); Associated with 3-methylglutaconic aciduria type 5.

**At a glance:** Likely benign · review: Multiple submitters · rsID rs367841424 · 3 submitters · 1 linked condition · ultra-rare (popmax 0.0196%, nfe)

## For patients & families {#patients}

This is a change in the DNAJC19 gene that is classified as likely benign — not considered disease-causing, submitted by 3 submitters, and is linked to 3-methylglutaconic aciduria type 5.

*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.*

|  |  |
| --- | --- |
| Typical inheritance (of this condition) | Autosomal recessive |
| Age of onset (of this condition) | Childhood, Infancy |
| Clinical trials | 1 registered for this condition — see ClinicalTrials.gov |
| Diagnostic panels | DNAJC19 is a diagnostic-grade gene on 15 Genomics England panels |

**Commonly reported features of Dilated cardiomyopathy with ataxia** (across patients with this condition; presentation varies — frequencies from Orphanet):

- Ataxia — Very frequent (99-80%)
- Growth delay — Very frequent (99-80%)
- Dilated cardiomyopathy — Very frequent (99-80%)
- Glutaric acidemia — Very frequent (99-80%)
- 3-Methylglutaconic aciduria — Very frequent (99-80%)
- Intrauterine growth retardation — Frequent (79-30%)
- Prolonged QT interval — Frequent (79-30%)
- Increased circulating lactate concentration — Frequent (79-30%)

**Support & next steps:** [Condition overview & support (NIH GARD)](https://rarediseases.info.nih.gov/diseases/0012964/index) · [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [DNAJC19](https://sugi.bio/atlas/gene/DNAJC19/) |
| Coding change (HGVS c.) | c.3+16C>T |
| MANE Select transcript | [NM_145261](https://www.ncbi.nlm.nih.gov/nuccore/NM_145261) |
| dbSNP | [rs367841424](https://www.ncbi.nlm.nih.gov/snp/rs367841424/) |
| Variant type | single nucleotide variant |
| Location | chr3:180989584-180989584 (GRCh38) |
| ClinVar | [VCV510883](https://www.ncbi.nlm.nih.gov/clinvar/variation/510883/) |

**All HGVS expressions:** `LRG_743:g.5191C>T`, `LRG_743t1:c.3+16C>T`, `NC_000003.11:g.180707372G>A`, `NC_000003.12:g.180989584G>A`, `NG_022933.1:g.5191C>T`, `NM_145261.4:c.3+16C>T`

## 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 (below), not from a missing predictor score.
- Conservation: phyloP -1.551 — not a conserved position (phyloP < 0.1, ACGS BP7 cut)
- CADD: **PHRED 0.887**. 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.*
- Splice region: **near-intronic (+16 nt from the splice site)**.
- Non-coding constraint (Gnocchi): **Z 1.05**, o/e 0.93 (1 kb window 180,989,000–180,990,000). A higher Z means the window carries less variation than expected. Describes the 1 kb window, not this allele. No ClinGen expert panel references Gnocchi and no ACMG-calibrated threshold exists for it. *Descriptive; no cut-point 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 (gnomAD v4.1): grpmax **0.0196%** (nfe) · FAF95 0.0175% · FAF99 0.0166% · 228/1,162,918 in the highest group · 262/1,580,138 alleles overall — ultra-rare (popmax 0.0196%, nfe).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| Ashkenazi Jewish (not grpmax-eligible) | 0.0625% | 1,601 |
| Remaining individuals (not grpmax-eligible) | 0.0245% | 4,077 |
| European (non-Finnish) (grpmax) | 0.0196% | 5,101 |
| African / African-American | 0.00135% | 74,244 |

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}

**DNAJC19** population constraint: LOEUF 1.547, pLI 7.1195e-05, missense-Z 1.0653. *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):

- **3-methylglutaconic aciduria type 5** — Definitive (AR)

## Protein context {#protein}


AlphaFold model confidence (whole protein): pLDDT 87.50, 56% of residues very-high.

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

*Describes the biological roles of DNAJC19 (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}

DNAJC19 participates in **1 Reactome pathway** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| [Mitochondrial protein import](https://reactome.org/content/detail/R-HSA-1268020) | electronic |

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

**Biological process:** visual perception, genitalia development.

## Clinical significance {#significance}

**Likely benign** — review status Multiple submitters *(criteria provided, multiple submitters, no conflicts)*, last evaluated 2026-01-27.

**Submitter consensus:** unanimous (3/3 Likely benign).

**Submission history:** 3 submissions (2017–2026); classifications have been stable.

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| GeneDx | Likely benign | criteria provided, single submitter | clinical testing | 2017-08-01 |
| Labcorp Genetics (formerly Invitae), Labcorp | Likely benign | criteria provided, single submitter | clinical testing | 2026-01-27 |
| Blueprint Genetics | Likely benign | criteria provided, single submitter | clinical testing | 2024-10-07 |

## Associated conditions {#conditions}

[3-methylglutaconic aciduria type 5](https://sugi.bio/atlas/disease/3-methylglutaconic-aciduria-type-5/).

**Reported phenotype names (ClinVar):** 3-methylglutaconic aciduria type 5, not specified, CARDIOMYOPATHY, DILATED, WITH ATAXIA, 3 alpha methylglutaconic aciduria type V, MGA 5, MGA, TYPE V, AllHighlyPenetrant.

## Similar variants {#similar}

Related DNAJC19 variant pages (same residue, condition, or type): [DNAJC19 c.130-1G>C](/variant/dnajc19-c-130-minus-1g-c), [DNAJC19 c.4-1G>A](/variant/dnajc19-c-4-minus-1g-a), [DNAJC19 c.55+1G>A](/variant/dnajc19-c-55-plus-1g-a), [DNAJC19 p.Ala25Thr](/variant/dnajc19-p-ala25thr), [DNAJC19 p.Ala73Thr](/variant/dnajc19-p-ala73thr), [DNAJC19 p.Arg84Gln](/variant/dnajc19-p-arg84gln), [DNAJC19 p.Gly68Asp](/variant/dnajc19-p-gly68asp), [DNAJC19 p.Gly68Ser](/variant/dnajc19-p-gly68ser).

### 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 510883). 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.*