# NM_015107.3(PHF8):c.912C>T (p.Ser304=)

https://sugi.bio/variant/phf8-p-ser304

## Summary

**PHF8 p.Ser304= (c.912C>T)** is classified **Likely benign** in PHF8 (ClinVar, Single submitter, 2 submitters; last evaluated 2017-05-26). Ultra-rare (popmax 0.0131%, amr); Associated with Inborn genetic diseases.

**At a glance:** Likely benign · review: Single submitter · rsID rs782306751 · 2 submitters · 1 linked condition · ultra-rare (popmax 0.0131%, amr)

## For patients & families {#patients}

This is a change in the PHF8 gene that is classified as likely benign — not considered disease-causing, submitted by 2 submitters, and is linked to Inborn genetic diseases.

*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 | [PHF8](https://sugi.bio/atlas/gene/PHF8/) |
| Protein change (HGVS p.) | p.Ser304= |
| Coding change (HGVS c.) | c.912C>T |
| MANE Select transcript | [NM_015107](https://www.ncbi.nlm.nih.gov/nuccore/NM_015107) |
| dbSNP | [rs782306751](https://www.ncbi.nlm.nih.gov/snp/rs782306751/) |
| Variant type | single nucleotide variant |
| Location | chrX:54011156-54011156 (GRCh38) |
| ClinVar | [VCV589586](https://www.ncbi.nlm.nih.gov/clinvar/variation/589586/) |

**All HGVS expressions:** `NC_000023.10:g.54037589G>A`, `NC_000023.11:g.54011156G>A`, `NG_021309.1:g.38981C>T`, `NM_001184896.1:c.1020C>T`, `NM_001184897.2:c.912C>T`, `NM_001184898.2:c.912C>T`, `NM_015107.3:c.912C>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 -0.295, GERP -5.8, phastCons 0.003 — not a conserved position (phyloP < 0.1, ACGS BP7 cut)
- CADD: **PHRED 5.958**. 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: **below the reporting threshold**. This position is scored for a different substitution (G>C, Δ0.27 donor gain), so this allele was evaluated and its deltas all fell under Δ0.2 — a prediction of no splicing effect for this allele, not a gap in our data. *No ACMG code assigned.*
- Population frequency (gnomAD v4.1): grpmax **0.0131%** (amr) · FAF95 0.00567% · FAF99 0.00387% · 6/45,971 in the highest group · 17/1,096,545 alleles overall — ultra-rare (popmax 0.0131%, amr).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| Admixed American (grpmax) | 0.0131% | 7,662 |
| African / African-American | 0.00173% | 57,803 |
| European (non-Finnish) | 0.00112% | 89,403 |

*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}

**PHF8** population constraint: ClinGen dosage — haploinsufficiency 3, triplosensitivity 0 (0–3 scale). *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):

- **syndromic X-linked intellectual disability Siderius type** — Definitive (XL)

## Protein context {#protein}

Residue **304** lies in the jmjc domain; a β-strand.

AlphaFold model confidence (whole protein): pLDDT 63.30, 36% of residues very-high.

**6 experimental structure(s)** (PDB): [2WWU](https://www.rcsb.org/structure/2WWU), [3K3N](https://www.rcsb.org/structure/3K3N), [3K3O](https://www.rcsb.org/structure/3K3O), [3KV4](https://www.rcsb.org/structure/3KV4), [4DO0](https://www.rcsb.org/structure/4DO0), [7CMZ](https://www.rcsb.org/structure/7CMZ).

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

*Describes the biological roles of PHF8 (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:** PHF8's established molecular role includes chromatin binding. p.Ser304= falls in the jmjc domain.


### Pathways affected {#pathways}

PHF8 participates in **2 Reactome pathways** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| [HDMs demethylate histones](https://reactome.org/content/detail/R-HSA-3214842) | curated |
| [Condensation of Prophase Chromosomes](https://reactome.org/content/detail/R-HSA-2299718) | other |

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

**Molecular function:** chromatin binding, iron ion binding, zinc ion binding, histone demethylase activity, histone H3K9 demethylase activity, histone H4K20 demethylase activity.

**Biological process:** G1/S transition of mitotic cell cycle, positive regulation of DNA-templated transcription, positive regulation of transcription by RNA polymerase I, positive regulation of transcription by RNA polymerase II, negative regulation of rDNA heterochromatin formation.

## Clinical significance {#significance}

**Likely benign** — review status Single submitter *(criteria provided, single submitter)*, last evaluated 2017-05-26.

**Submitter consensus:** unanimous (2/2 Likely benign).

**Submission history:** 2 submissions (2017–2024); classifications have been stable.

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Ambry Genetics | Likely benign | criteria provided, single submitter | clinical testing | 2017-05-26 |
| PreventionGenetics, part of Exact Sciences | Likely benign | no assertion criteria provided | clinical testing | 2024-02-15 |

## Associated conditions {#conditions}

[Inborn genetic diseases](https://sugi.bio/atlas/disease/inborn-genetic-diseases/).

**Reported phenotype names (ClinVar):** Inborn genetic diseases, PHF8-related disorder, PHF8-related condition.

## Similar variants {#similar}

Related PHF8 variant pages (same residue, condition, or type): [PHF8 p.Arg506Ter](/variant/phf8-p-arg506ter), [PHF8 p.Ala770Pro](/variant/phf8-p-ala770pro), [PHF8 p.Arg240Gln](/variant/phf8-p-arg240gln), [PHF8 p.Arg438His](/variant/phf8-p-arg438his), [PHF8 p.Arg588Gln](/variant/phf8-p-arg588gln), [PHF8 p.Arg773Pro](/variant/phf8-p-arg773pro), [PHF8 p.Arg968Cys](/variant/phf8-p-arg968cys), [PHF8 p.Arg982Trp](/variant/phf8-p-arg982trp).

### Data sources & attribution {#sources}

ClinVar (NCBI — public domain, built 2026-10-14); 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 589586). 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.*