# NM_015214.3(DDHD2):c.1009A>C (p.Arg337=)

https://sugi.bio/variant/ddhd2-p-arg337

## Summary

**DDHD2 p.Arg337= (c.1009A>C)** is classified **Conflicting classifications of pathogenicity** in DDHD2 (ClinVar, Conflicting submitters, 4 submitters; last evaluated 2024-10-31). Ultra-rare (popmax 0.0111%, nfe); Associated with hereditary spastic paraplegia.

**At a glance:** Conflicting classifications of pathogenicity · review: Conflicting submitters · rsID rs778628163 · 4 submitters · 2 linked conditions · ultra-rare (popmax 0.0111%, nfe)

## For patients & families {#patients}

This is a change in the DDHD2 gene that is of uncertain or conflicting significance (submitters disagree on it), submitted by 4 submitters, and is linked to hereditary spastic paraplegia.

*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.*

|  |  |
| --- | --- |
| Clinical trials | 55 registered for this condition — see ClinicalTrials.gov |

**Support & next steps:** [Condition overview & support (NIH GARD)](https://rarediseases.info.nih.gov/diseases/0006637/index) · [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [DDHD2](https://sugi.bio/atlas/gene/DDHD2/) |
| Protein change (HGVS p.) | p.Arg337= |
| Coding change (HGVS c.) | c.1009A>C |
| MANE Select transcript | [NM_015214](https://www.ncbi.nlm.nih.gov/nuccore/NM_015214) |
| dbSNP | [rs778628163](https://www.ncbi.nlm.nih.gov/snp/rs778628163/) |
| Variant type | single nucleotide variant |
| Location | chr8:38245902-38245902 (GRCh38) |
| ClinVar | [VCV381854](https://www.ncbi.nlm.nih.gov/clinvar/variation/381854/) |

**All HGVS expressions:** `NC_000008.10:g.38103420A>C`, `NC_000008.11:g.38245902A>C`, `NG_033875.1:g.19412A>C`, `NM_001164232.2:c.1009A>C`, `NM_001362911.2:c.1009A>C`, `NM_001362912.2:c.1009A>C`, `NM_001362913.2:c.919A>C`, `NM_001362914.2:c.1009A>C`, `NM_015214.3:c.1009A>C`, `NR_156416.2:n.1292A>C`, `NR_156417.2:n.1292A>C`

## 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 6.96, GERP -0.692, phastCons 1 — highly conserved position (PP3-type support)
- CADD: **PHRED 12.26**. 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: **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 **0.0111%** (nfe) · FAF95 0.00952% · FAF99 0.00896% · 131/1,180,048 in the highest group · 146/1,613,952 alleles overall — ultra-rare (popmax 0.0111%, nfe).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| Remaining individuals (not grpmax-eligible) | 0.0192% | 5,207 |
| European (non-Finnish) (grpmax) | 0.0111% | 9,008 |
| African / African-American | 0.00267% | 37,464 |
| Admixed American | 0.00167% | 59,996 |

Remaining individuals 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}

**DDHD2** population constraint: LOEUF 0.758, pLI 1.2846e-06, missense-Z 1.7398. *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 **337** lies in a UniProt-annotated variant site (in spg54; likely pathogenic; loss of triacylglycerol hydrolase activity).

AlphaFold model confidence (whole protein): pLDDT 74.70, 36% of residues very-high.

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

*Describes the biological roles of DDHD2 (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}

DDHD2 participates in **1 Reactome pathway** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| [Synthesis of PA](https://reactome.org/content/detail/R-HSA-1483166) | curated |

## Clinical significance {#significance}

**Conflicting classifications of pathogenicity** — review status Conflicting submitters *(criteria provided, conflicting classifications)*, last evaluated 2024-10-31.

**Submitter consensus:** conflicting (2 Likely benign, 2 Uncertain significance).

**Submission history:** 4 submissions (2016–2024); classifications have differed over time.

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| GeneDx | Likely benign | criteria provided, single submitter | clinical testing | 2016-01-20 |
| Genetic Services Laboratory, University of Chicago | Uncertain significance | criteria provided, single submitter | clinical testing | 2019-09-24 |
| Genome Diagnostics Laboratory, The Hospital for Sick Children | Uncertain significance | criteria provided, single submitter | clinical testing | 2017-06-22 |
| Labcorp Genetics (formerly Invitae), Labcorp | Likely benign | criteria provided, single submitter | clinical testing | 2024-10-31 |

## Associated conditions {#conditions}

[hereditary spastic paraplegia](https://sugi.bio/atlas/disease/hereditary-spastic-paraplegia/), [hereditary spastic paraplegia 54](https://sugi.bio/atlas/disease/hereditary-spastic-paraplegia-54/).

**Reported phenotype names (ClinVar):** Hereditary spastic paraplegia, not specified, Hereditary spastic paraplegia 54, AllHighlyPenetrant, Familial spastic paraparesis, Spastic paraplegia 54, autosomal recessive.

## Similar variants {#similar}

Related DDHD2 variant pages (same residue, condition, or type): [DDHD2 c.1126-2A>G](/variant/ddhd2-c-1126-minus-2a-g), [DDHD2 c.1248+2T>C](/variant/ddhd2-c-1248-plus-2t-c), [DDHD2 p.Arg232Ter](/variant/ddhd2-p-arg232ter), [DDHD2 p.Arg329Ter](/variant/ddhd2-p-arg329ter), [DDHD2 p.Arg516Ter](/variant/ddhd2-p-arg516ter), [DDHD2 p.Asp660His](/variant/ddhd2-p-asp660his), [DDHD2 p.Gln286Ter](/variant/ddhd2-p-gln286ter), [DDHD2 p.Trp115Ter](/variant/ddhd2-p-trp115ter).

### 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 381854). 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.*