# NM_001303256.3(MORC2):c.1437A>G (p.Pro479=)

https://sugi.bio/variant/morc2-p-pro479

## Summary

**MORC2 p.Pro479= (c.1437A>G)** is classified **Benign** in MORC2 (ClinVar, Multiple submitters, 5 submitters; last evaluated 2026-02-04). Common (popmax 63.2%, eas) — too common for a highly-penetrant pathogenic allele; Associated with developmental delay, impaired growth, dysmorphic facies, and axonal neuropathy.

**At a glance:** Benign · review: Multiple submitters · rsID rs3747151 · 5 submitters · 2 linked conditions · common (popmax 63.2%, eas) — too common for a highly-penetrant pathogenic allele

## For patients & families {#patients}

This is a change in the MORC2 gene that is classified as benign — not considered disease-causing, submitted by 5 submitters, and is linked to developmental delay, impaired growth, dysmorphic facies, and axonal neuropathy.

*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 | [MORC2](https://sugi.bio/atlas/gene/MORC2/) |
| Protein change (HGVS p.) | p.Pro479= |
| Coding change (HGVS c.) | c.1437A>G |
| MANE Select transcript | [NM_001303256](https://www.ncbi.nlm.nih.gov/nuccore/NM_001303256) |
| dbSNP | [rs3747151](https://www.ncbi.nlm.nih.gov/snp/rs3747151/) |
| Variant type | single nucleotide variant |
| Location | chr22:30937644-30937644 (GRCh38) |
| ClinVar | [VCV1168329](https://www.ncbi.nlm.nih.gov/clinvar/variation/1168329/) |

**All HGVS expressions:** `NC_000022.10:g.31333631T>C`, `NC_000022.11:g.30937644T>C`, `NG_046752.1:g.35854A>G`, `NM_001303256.3:c.1437A>G`, `NM_001303257.2:c.1437A>G`, `NM_014941.3:c.1251A>G`

## Computational & population evidence {#evidence}

**Concordance:** Evidence sources **disagree** — common (popmax 63.2%, eas) — 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 -2.232, GERP -3.2 — fast-evolving / accelerated position
- CADD: **PHRED 8.755**. 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: **no splice effect predicted**. SpliceAI outputs four numbers per variant, not one: acceptor loss, donor loss, acceptor gain, donor gain (DS_AL / DS_DL / DS_AG / DS_DG). A loss score is an existing splice site weakened or destroyed; a gain score is a new site created or an existing one strengthened. The release publishes its own filter rule, which we read from the dataset rather than assume: an allele is reported only if the largest of its four deltas reaches 0.2. No allele at this position is in the release, so all four are under 0.2 for every alternate allele here. No figure is shown because none was read: the bound is deduced from that absence. It is a result, not a gap in our data, because the release scores every possible substitution across the transcripts it covers (Ensembl MANE v1.4) before it filters, so what survives for a gene is one continuous stretch. What is measured is that this position sits inside the stretch covered for MORC2 (1,332 scored positions, the nearest 10 bases away); what is taken from the release's own description, rather than measured, is that coverage inside that stretch is continuous. On that, SpliceAI did score it. *ClinGen's SVI treats the largest of the four as evidence against a splicing effect at or below 0.1, where it may support BP4, and as uninformative between 0.1 and 0.2. We cannot tell which applies here, so these SpliceAI data support neither BP4 nor PP3; that is a statement about this evidence alone, not about the variant's other evidence.*
- Population frequency (gnomAD v4.1): grpmax **63.2%** (eas) · FAF95 62.6% · FAF99 62.4% · 28,359/44,856 in the highest group · 543,326/1,613,566 alleles overall — common (popmax 63.2%, eas) — too common for a highly-penetrant pathogenic allele.

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| East Asian (grpmax) | 63.2% | 2 |
| African / African-American | 55.4% | 2 |
| Remaining individuals (not grpmax-eligible) | 35.3% | 3 |
| Ashkenazi Jewish (not grpmax-eligible) | 33.3% | 3 |
| Finnish (not grpmax-eligible) | 32.2% | 3 |
| Admixed American | 32% | 3 |
| European (non-Finnish) | 31.6% | 3 |
| Middle Eastern | 30.9% | 3 |
| South Asian | 29.5% | 3 |
| Amish (not grpmax-eligible) | 29.3% | 3 |

*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}

**MORC2** population constraint: LOEUF 0.3, pLI 1, missense-Z 4.4514. *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):

- **Leigh syndrome** — Limited (AD)
- **Charcot-Marie-Tooth disease axonal type 2Z** — Definitive (AD)

## Protein context {#protein}

Residue **479** lies in an α-helix.

AlphaFold model confidence (whole protein): pLDDT 78.37, 52% of residues very-high.

**9 experimental structure(s)** (PDB): [5OF9](https://www.rcsb.org/structure/5OF9), [5OFA](https://www.rcsb.org/structure/5OFA), [5OFB](https://www.rcsb.org/structure/5OFB), [9CDF](https://www.rcsb.org/structure/9CDF), [9CDG](https://www.rcsb.org/structure/9CDG), [9CDH](https://www.rcsb.org/structure/9CDH) — incl. mutant structure 9CDF.

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

*Describes the biological roles of MORC2 (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:** MORC2's established molecular role includes magnesium ion binding.


### Pathways affected {#pathways}

MORC2 participates in **2 Reactome pathways** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| [Fatty acyl-CoA biosynthesis](https://reactome.org/content/detail/R-HSA-75105) | curated |
| [Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex](https://reactome.org/content/detail/R-HSA-9843970) | electronic |

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

**Molecular function:** magnesium ion binding, chromatin binding, ATP binding, zinc ion binding, ATP hydrolysis activity, protein homodimerization activity.

**Biological process:** chromatin remodeling, DNA damage response, constitutive heterochromatin formation, transposable element silencing by heterochromatin formation.

## Clinical significance {#significance}

**Benign** — review status Multiple submitters *(criteria provided, multiple submitters, no conflicts)*, last evaluated 2026-02-04.

**Submitter consensus:** unanimous (6/6 Benign).

**Submission history:** 6 submissions (2018–2026); classifications have been stable.

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| GeneDx | Benign | criteria provided, single submitter | clinical testing | 2018-07-05 |
| Genome-Nilou Lab | Benign | criteria provided, single submitter | clinical testing | 2022-03-15 |
| Breakthrough Genomics, Breakthrough Genomics | Benign | criteria provided, single submitter | not provided |  |
| Mayo Clinic Laboratories, Mayo Clinic | Benign | criteria provided, single submitter | clinical testing | 2022-03-24 |
| Labcorp Genetics (formerly Invitae), Labcorp | Benign | criteria provided, single submitter | clinical testing | 2026-02-04 |

## Associated conditions {#conditions}

[developmental delay, impaired growth, dysmorphic facies, and axonal neuropathy](https://sugi.bio/atlas/disease/developmental-delay-impaired-growth-dysmorphic-facies-and-axonal-neuropathy/), [Charcot-Marie-Tooth disease axonal type 2Z](https://sugi.bio/atlas/disease/charcot-marie-tooth-disease-axonal-type-2z/).

**Reported phenotype names (ClinVar):** Developmental delay, impaired growth, dysmorphic facies, and axonal neuropathy, Charcot-Marie-Tooth disease axonal type 2Z, not provided, not specified, CHARCOT-MARIE-TOOTH DISEASE, AXONAL, AUTOSOMAL DOMINANT, TYPE 2Z, CHARCOT-MARIE-TOOTH NEUROPATHY, TYPE 2Z, AllHighlyPenetrant, none provided.

## Similar variants {#similar}

Related MORC2 variant pages (same residue, condition, or type): [MORC2 p.Arg132Cys](/variant/morc2-p-arg132cys), [MORC2 p.Arg132His](/variant/morc2-p-arg132his), [MORC2 p.Arg252Trp](/variant/morc2-p-arg252trp), [MORC2 p.Arg266Ser](/variant/morc2-p-arg266ser), [MORC2 p.Asp466Asn](/variant/morc2-p-asp466asn), [MORC2 p.Glu236Gly](/variant/morc2-p-glu236gly), [MORC2 p.Glu27Lys](/variant/morc2-p-glu27lys), [MORC2 p.Ser87Leu](/variant/morc2-p-ser87leu).

### Data sources & attribution {#sources}

ClinVar (NCBI — public domain, built 2026-10-14); gnomAD v4.1 (Broad Institute, built 2026-10-15); 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 1168329). 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.*