# NM_004426.3(PHC1):c.918A>G (p.Arg306=)

https://sugi.bio/variant/phc1-p-arg306

## Summary

**PHC1 p.Arg306= (c.918A>G)** is classified **Benign** in PHC1 (ClinVar, Multiple submitters, 4 submitters; last evaluated 2021-09-05). Common (popmax 96.4%, sas) — too common for a highly-penetrant pathogenic allele; Associated with microcephaly 11, primary, autosomal recessive.

**At a glance:** Benign · review: Multiple submitters · rsID rs1805777 · 4 submitters · 1 linked condition · common (popmax 96.4%, sas) — too common for a highly-penetrant pathogenic allele

## For patients & families {#patients}

This is a change in the PHC1 gene that is classified as benign — not considered disease-causing, submitted by 4 submitters, and is linked to microcephaly 11, primary, autosomal recessive.

*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/0024977/index) · [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [PHC1](https://sugi.bio/atlas/gene/PHC1/) |
| Protein change (HGVS p.) | p.Arg306= |
| Coding change (HGVS c.) | c.918A>G |
| MANE Select transcript | [NM_004426](https://www.ncbi.nlm.nih.gov/nuccore/NM_004426) |
| dbSNP | [rs1805777](https://www.ncbi.nlm.nih.gov/snp/rs1805777/) |
| Variant type | single nucleotide variant |
| Location | chr12:8930740-8930740 (GRCh38) |
| ClinVar | [VCV211899](https://www.ncbi.nlm.nih.gov/clinvar/variation/211899/) |

**All HGVS expressions:** `NC_000012.11:g.9083336A>G`, `NC_000012.12:g.8930740A>G`, `NG_042273.1:g.21021A>G`, `NM_004426.3:c.918A>G`

## Computational & population evidence {#evidence}

**Concordance:** Evidence sources **disagree** — common (popmax 96.4%, sas) — too common for a highly-penetrant pathogenic allele.

- **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 3.062, GERP -0.117, phastCons 1 — highly conserved position (PP3-type support)
- CADD: **PHRED 10.03**. 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 **96.4%** (sas) · FAF95 95.8% · FAF99 95.5% · 64,293/66,700 in the highest group · 1,097,284/1,188,302 alleles overall — common (popmax 96.4%, sas) — too common for a highly-penetrant pathogenic allele.

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| South Asian (grpmax) | 96.4% | 1 |
| Finnish (not grpmax-eligible) | 96% | 1 |
| Amish (not grpmax-eligible) | 95% | 1 |
| European (non-Finnish) | 95% | 1 |
| Ashkenazi Jewish (not grpmax-eligible) | 92% | 1 |
| Remaining individuals (not grpmax-eligible) | 90.9% | 1 |
| Middle Eastern | 90.7% | 1 |
| Admixed American | 89.7% | 1 |
| East Asian | 76.9% | 1 |
| African / African-American | 62.2% | 2 |

*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}

**PHC1** population constraint: LOEUF 0.322, pLI 1, missense-Z 2.7357; ClinGen dosage — haploinsufficiency gene assoc. with recessive phenotype, triplosensitivity 0/3. *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 **306** lies in the 'disordered' region.

AlphaFold model confidence (whole protein): pLDDT 51.06, 9% of residues very-high.

**1 experimental structure(s)** (PDB): [2L8E](https://www.rcsb.org/structure/2L8E).

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

*Describes the biological roles of PHC1 (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}

PHC1 participates in **10 Reactome pathways** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| [Oxidative Stress Induced Senescence](https://reactome.org/content/detail/R-HSA-2559580) | curated |
| [RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known](https://reactome.org/content/detail/R-HSA-8939243) | curated |
| [SUMOylation of DNA damage response and repair proteins](https://reactome.org/content/detail/R-HSA-3108214) | curated |
| [SUMOylation of RNA binding proteins](https://reactome.org/content/detail/R-HSA-4570464) | curated |
| [SUMOylation of chromatin organization proteins](https://reactome.org/content/detail/R-HSA-4551638) | curated |
| [SUMOylation of transcription cofactors](https://reactome.org/content/detail/R-HSA-3899300) | curated |
| [Transcriptional Regulation by E2F6](https://reactome.org/content/detail/R-HSA-8953750) | curated |
| [Differentiation of naive CD4+ T cells to T helper 2 cells (Th2 cells)](https://reactome.org/content/detail/R-HSA-9976102) | electronic |
| [Regulation of PTEN gene transcription](https://reactome.org/content/detail/R-HSA-8943724) | electronic |
| [SUMOylation of DNA methylation proteins](https://reactome.org/content/detail/R-HSA-4655427) | electronic |

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

**Biological process:** chromatin remodeling.

## Clinical significance {#significance}

**Benign** — review status Multiple submitters *(criteria provided, multiple submitters, no conflicts)*, last evaluated 2021-09-05.

**Submitter consensus:** unanimous (4/4 Benign).

**Submission history:** 4 submissions (2015–2021); classifications have been stable.

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Genetic Services Laboratory, University of Chicago | Benign | criteria provided, single submitter | clinical testing | 2015-02-17 |
| GeneDx | Benign | criteria provided, single submitter | clinical testing | 2021-06-09 |
| Genome-Nilou Lab | Benign | criteria provided, single submitter | clinical testing | 2021-09-05 |
| Breakthrough Genomics, Breakthrough Genomics | Benign | criteria provided, single submitter | not provided |  |

## Associated conditions {#conditions}

[microcephaly 11, primary, autosomal recessive](https://sugi.bio/atlas/disease/microcephaly-11-primary-autosomal-recessive/).

**Reported phenotype names (ClinVar):** Microcephaly 11, primary, autosomal recessive, not specified, not provided, none provided, AllHighlyPenetrant.

## Similar variants {#similar}

Related PHC1 variant pages (same residue, condition, or type): [PHC1 p.Arg876Trp](/variant/phc1-p-arg876trp), [PHC1 c.2860+12C>T](/variant/phc1-c-2860-plus-12c-t), [PHC1 p.Leu31=](/variant/phc1-p-leu31), [PHC1 p.Pro123=](/variant/phc1-p-pro123), [PHC1 p.Thr693Ala](/variant/phc1-p-thr693ala), [PHC1 p.Arg34Ter](/variant/phc1-p-arg34ter), [PHC1 p.Met593Leu](/variant/phc1-p-met593leu), [PHC1 p.Pro24Leu](/variant/phc1-p-pro24leu).

### 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 211899). 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.*