# NM_003002.4(SDHD):c.424_427del (p.Phe142fs)

https://sugi.bio/variant/sdhd-p-phe142fs

## Summary

**SDHD p.Phe142fs (c.424_427del)** is classified **Likely pathogenic** in SDHD (ClinVar, Single submitter, 1 submitter; last evaluated 2022-01-03). No gnomAD frequency available for this variant; Associated with pheochromocytoma/paraganglioma syndrome 1.

**At a glance:** Likely pathogenic · review: Single submitter · rsID rs2135277706 · 1 submitter · 1 linked condition · no gnomAD frequency available for this variant

## For patients & families {#patients}

This is a change in the SDHD gene that is considered likely disease-causing, submitted by 1 submitter, and is linked to pheochromocytoma/paraganglioma syndrome 1.

*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/0007324/index) · [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [SDHD](https://sugi.bio/atlas/gene/SDHD/) |
| Protein change (HGVS p.) | p.Phe142fs |
| Coding change (HGVS c.) | c.424_427del |
| MANE Select transcript | [NM_003002](https://www.ncbi.nlm.nih.gov/nuccore/NM_003002) |
| dbSNP | [rs2135277706](https://www.ncbi.nlm.nih.gov/snp/rs2135277706/) |
| Variant type | Deletion |
| Location | chr11:112094914-112094917 (GRCh38) |
| ClinVar | [VCV1333204](https://www.ncbi.nlm.nih.gov/clinvar/variation/1333204/) |

**All HGVS expressions:** `LRG_9:g.13068_13071del`, `LRG_9t1:c.424_427del`, `NC_000011.10:g.112094914_112094917del`, `NC_000011.9:g.111965638_111965641del`, `NG_012337.3:g.13068_13071del`, `NM_001276503.2:c.*21_*24del`, `NM_001276504.2:c.307_310del`, `NM_001276506.2:c.*122_*125del`, `NM_003002.4:c.424_427del`, `NR_077060.2:n.513_516del`

## 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 -0.772, GERP -4.28, phastCons 0.017 — not a conserved position (phyloP < 0.1, ACGS BP7 cut)
- Molecular consequence: **frameshift** — a predicted loss-of-function variant. ClinGen curates **sufficient evidence for haploinsufficiency** in this gene (constraint LOEUF 0.581, pLI 0.90513), supporting a loss-of-function disease mechanism. *Descriptive; not an applied PVS1 code.*
- Nonsense-mediated decay: the premature termination codon is **in the last exon (4 of 4)** — predicted to **escape NMD**, so the truncated protein is likely expressed. An input to PVS1, not an applied code.
- SpliceAI: **not assessed** — the release is built from a substitutions-only source, so it holds no deletion variants. That is a property of the dataset, not of the variant, and is not evidence against a splicing effect.
- Population frequency: **no gnomAD frequency available for this variant** — rarity (ACMG PM2) and BA1/BS1 cannot be assessed for this variant.

*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}

**SDHD** population constraint: LOEUF 0.581, pLI 0.90513, missense-Z 0.80794; ClinGen dosage — haploinsufficiency 3/3, triplosensitivity 0/3. *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):

- **mitochondrial disease** — Limited (AR)
- **hereditary pheochromocytoma-paraganglioma** — Definitive (AD)

## Protein context {#protein}

Residue **142** lies in an α-helix.

AlphaFold model confidence (whole protein): pLDDT 81.50, 63% of residues very-high.

**2 experimental structure(s)** (PDB): [8GS8](https://www.rcsb.org/structure/8GS8), [9KC4](https://www.rcsb.org/structure/9KC4).

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

*Describes the biological roles of SDHD (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}

SDHD participates in **3 Reactome pathways** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| [Citric acid cycle (TCA cycle)](https://reactome.org/content/detail/R-HSA-71403) | curated |
| [Maturation of TCA enzymes and regulation of TCA cycle](https://reactome.org/content/detail/R-HSA-9854311) | curated |
| [Respiratory electron transport](https://reactome.org/content/detail/R-HSA-611105) | electronic |

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

**Biological process:** tricarboxylic acid cycle.

## Clinical significance {#significance}

**Likely pathogenic** — review status Single submitter *(criteria provided, single submitter)*, last evaluated 2022-01-03.

**Submitter consensus:** unanimous (1/1 Likely pathogenic).

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| 3billion | Likely pathogenic | criteria provided, single submitter | clinical testing | 2022-01-03 |

## Associated conditions {#conditions}

[pheochromocytoma/paraganglioma syndrome 1](https://sugi.bio/atlas/disease/pheochromocytoma-paraganglioma-syndrome-1/).

**Reported phenotype names (ClinVar):** Pheochromocytoma/paraganglioma syndrome 1, Paragangliomas 1, Glomus tumors familial 1, PARAGANGLIOMATA, PARAGANGLIOMAS, FAMILIAL NONCHROMAFFIN, 1, PGL 1, Paragangliomas familial 1, Paraganglioma - glomus jugulare, SDHD-Related Hereditary Paraganglioma-Pheochromocytoma Syndrome.

## Similar variants {#similar}

Related SDHD variant pages (same residue, condition, or type): [SDHD p.Gly58fs](/variant/sdhd-p-gly58fs), [SDHD p.Leu20fs](/variant/sdhd-p-leu20fs), [SDHD p.Pro81fs](/variant/sdhd-p-pro81fs), [SDHD p.Ser132fs](/variant/sdhd-p-ser132fs), [SDHD p.Phe142Leu](/variant/sdhd-p-phe142leu), [SDHD c.315-13del](/variant/sdhd-c-315-minus-13del), [SDHD p.Arg38fs](/variant/sdhd-p-arg38fs), [SDHD p.Gly148fs](/variant/sdhd-p-gly148fs).

### Data sources & attribution {#sources}

ClinVar (NCBI — public domain, built 2026-10-14); gnomAD v4.1 (Broad Institute, built 2026-10-14); 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 1333204). 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.*