# NM_001378964.1(CDON):c.173G>A (p.Arg58His)

https://sugi.bio/variant/cdon-p-arg58his

## Summary

**CDON p.Arg58His (c.173G>A)** is classified **Conflicting classifications of pathogenicity** in CDON (ClinVar, Conflicting submitters, 3 submitters; last evaluated 2024-10-14). AlphaMissense: likely benign (0.0976); Very rare (popmax 0.005%, amr); Associated with holoprosencephaly 11.

**At a glance:** Conflicting classifications of pathogenicity · review: Conflicting submitters · rsID rs377281257 · 3 submitters · 1 linked condition · AlphaMissense likely benign · very rare (popmax 0.005%, amr)

## For patients & families {#patients}

This is a change in the CDON gene that is of uncertain or conflicting significance (submitters disagree on it), submitted by 3 submitters, and is linked to holoprosencephaly 11.

*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/0024938/index) · [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [CDON](https://sugi.bio/atlas/gene/CDON/) |
| Protein change (HGVS p.) | p.Arg58His |
| Coding change (HGVS c.) | c.173G>A |
| MANE Select transcript | [NM_001378964](https://www.ncbi.nlm.nih.gov/nuccore/NM_001378964) |
| dbSNP | [rs377281257](https://www.ncbi.nlm.nih.gov/snp/rs377281257/) |
| Variant type | single nucleotide variant |
| Location | chr11:126021424-126021424 (GRCh38) |
| ClinVar | [VCV2072075](https://www.ncbi.nlm.nih.gov/clinvar/variation/2072075/) |

**All HGVS expressions:** `NC_000011.10:g.126021424C>T`, `NC_000011.9:g.125891319C>T`, `NG_029776.1:g.46869G>A`, `NM_001243597.3:c.173G>A`, `NM_001378964.1:c.173G>A`, `NM_016952.6:c.173G>A`

## Computational & population evidence {#evidence}

**Concordance:** Mixed / partial computational evidence (see below).

- AlphaMissense **likely benign** (0.0976)
- REVEL 0.045 (moderately benign-leaning) — agrees with AlphaMissense
- SaProt LLR -4.777 (tolerated) — agrees with AlphaMissense
- → **In-silico consensus:** AlphaMissense, REVEL and SaProt all call this tolerated
- Conservation: phyloP -2.121, GERP -2.44 — fast-evolving / accelerated position
- CADD: **PHRED 11.13**. 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.*
- Regional missense constraint: **o/e 0.93** across the covering region of the MANE Select transcript (125,960,945–126,023,476), spanning 62,531 bp. Chi-square p 0.0032. Describes the region, not this allele; gnomAD v4.1.1's own constrained determination. *Descriptive; no ACMG code 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 **0.005%** (amr) · FAF95 0.00133% · FAF99 0.000668% · 3/60,006 in the highest group · 12/1,613,938 alleles overall — very rare (popmax 0.005%, amr).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| Admixed American (grpmax) | 0.005% | 20,002 |
| South Asian | 0.0022% | 45,535 |
| Remaining individuals (not grpmax-eligible) | 0.0016% | 62,484 |
| European (non-Finnish) | 0.000508% | 196,664 |

*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}

**CDON** population constraint: LOEUF 0.733, pLI 4.8789e-12, missense-Z 1.7698. *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 **58** lies in a disulfide bond; the ig-like c2-type 1 domain.

AlphaFold model confidence (whole protein): pLDDT 62.62, 11% of residues very-high.

**3 experimental structure(s)** (PDB): [3D1M](https://www.rcsb.org/structure/3D1M), [3N1F](https://www.rcsb.org/structure/3N1F), [3N1Q](https://www.rcsb.org/structure/3N1Q).

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

*Describes the biological roles of CDON (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:** CDON's established molecular role includes coreceptor activity. p.Arg58His falls in the ig-like c2-type 1 domain.


### Pathways affected {#pathways}

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

| Pathway (Reactome) | Evidence |
| --- | --- |
| [Activation of SMO](https://reactome.org/content/detail/R-HSA-5635838) | curated |
| [Ligand-receptor interactions](https://reactome.org/content/detail/R-HSA-5632681) | curated |
| [Myogenesis](https://reactome.org/content/detail/R-HSA-525793) | electronic |

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

**Molecular function:** coreceptor activity.

**Biological process:** smoothened signaling pathway.

## Clinical significance {#significance}

**Conflicting classifications of pathogenicity** — review status Conflicting submitters *(criteria provided, conflicting classifications)*, last evaluated 2024-10-14.

**Submitter consensus:** conflicting (2 Uncertain significance, 1 Likely benign).

**Submission history:** 3 submissions (2021–2024); classifications have differed over time.

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Uncertain significance | criteria provided, single submitter | clinical testing | 2023-12-26 |
| Ambry Genetics | Likely benign | criteria provided, single submitter | clinical testing | 2021-07-14 |
| Labcorp Genetics (formerly Invitae), Labcorp | Uncertain significance | criteria provided, single submitter | clinical testing | 2024-10-14 |

## Associated conditions {#conditions}

[holoprosencephaly 11](https://sugi.bio/atlas/disease/holoprosencephaly-11/).

**Reported phenotype names (ClinVar):** Holoprosencephaly 11, Inborn genetic diseases, not specified, AllHighlyPenetrant.

## Similar variants {#similar}

Related CDON variant pages (same residue, condition, or type): [CDON c.3276+1G>T](/variant/cdon-c-3276-plus-1g-t), [CDON c.640+1G>A](/variant/cdon-c-640-plus-1g-a), [CDON c.*1805A>G](/variant/cdon-c-star-1805a-g), [CDON c.*1816C>T](/variant/cdon-c-star-1816c-t), [CDON c.*2349A>C](/variant/cdon-c-star-2349a-c), [CDON c.*2377T>C](/variant/cdon-c-star-2377t-c), [CDON c.*2760A>G](/variant/cdon-c-star-2760a-g), [CDON p.Ala1099Val](/variant/cdon-p-ala1099val).

### 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 2072075). 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.*