# NM_153717.3(EVC):c.456G>A (p.Pro152=)

https://sugi.bio/variant/evc-p-pro152

## Summary

**EVC p.Pro152= (c.456G>A)** is classified **Likely benign** in EVC (ClinVar, Single submitter, 1 submitter; last evaluated 2025-10-08). Very rare (popmax 0.00333%, amr); Associated with Ellis-van Creveld syndrome.

**At a glance:** Likely benign · review: Single submitter · rsID rs776773987 · 1 submitter · 2 linked conditions · very rare (popmax 0.00333%, amr)

## For patients & families {#patients}

This is a change in the EVC gene that is classified as likely benign — not considered disease-causing, submitted by 1 submitter, and is linked to Ellis-van Creveld syndrome.

*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/0001301/index) · [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [EVC](https://sugi.bio/atlas/gene/EVC/) |
| Protein change (HGVS p.) | p.Pro152= |
| Coding change (HGVS c.) | c.456G>A |
| MANE Select transcript | [NM_153717](https://www.ncbi.nlm.nih.gov/nuccore/NM_153717) |
| dbSNP | [rs776773987](https://www.ncbi.nlm.nih.gov/snp/rs776773987/) |
| Variant type | single nucleotide variant |
| Location | chr4:5731496-5731496 (GRCh38) |
| ClinVar | [VCV1122054](https://www.ncbi.nlm.nih.gov/clinvar/variation/1122054/) |

**All HGVS expressions:** `NC_000004.11:g.5733223G>A`, `NC_000004.12:g.5731496G>A`, `NG_008843.1:g.25300G>A`, `NM_001306090.2:c.456G>A`, `NM_001306092.2:c.456G>A`, `NM_153717.3:c.456G>A`

## 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 and, for splice-region changes, SpliceAI (below), not from a missing predictor score.
- SpliceAI predicts **acceptor gain** (Δ 0.30) — a splice-altering prediction the current classification does not reflect
- Conservation: phyloP -7.778, GERP -3.36 — fast-evolving / accelerated position
- CADD: **PHRED 6.399**. 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 deltas (raw): acceptor loss **0.06**, donor loss **0.00**, acceptor gain **0.30**, donor gain **0.00**. Largest is acceptor gain.
- SpliceAI deltas (masked): acceptor loss **0.00**, donor loss **0.00**, acceptor gain **0.30**, donor gain **0.00**.
- Population frequency (gnomAD v4.1): grpmax **0.00333%** (amr) · FAF95 0.00207% · FAF99 0.00183% · 2/59,990 in the highest group · 39/1,613,966 alleles overall — very rare (popmax 0.00333%, amr).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| Admixed American (grpmax) | 0.00333% | 29,995 |
| European (non-Finnish) | 0.00288% | 34,706 |
| Remaining individuals (not grpmax-eligible) | 0.0016% | 62,486 |
| African / African-American | 0.00134% | 74,894 |
| South Asian | 0.0011% | 91,070 |

*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}

**EVC** population constraint: LOEUF 1.134, pLI 6.2955e-37, missense-Z -1.5572. *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):

- **Ellis-van Creveld syndrome** — Definitive (AR)

## Protein context {#protein}

Residue **152** lies in the 'disordered' region.

AlphaFold model confidence (whole protein): pLDDT 74.49, 41% of residues very-high.

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

*Describes the biological roles of EVC (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}

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

| Pathway (Reactome) | Evidence |
| --- | --- |
| [Hedgehog 'on' state](https://reactome.org/content/detail/R-HSA-5632684) | curated |
| [Activation of SMO](https://reactome.org/content/detail/R-HSA-5635838) | electronic |

## Clinical significance {#significance}

**Likely benign** — review status Single submitter *(criteria provided, single submitter)*, last evaluated 2025-10-08.

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

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Labcorp Genetics (formerly Invitae), Labcorp | Likely benign | criteria provided, single submitter | clinical testing | 2025-10-08 |

## Associated conditions {#conditions}

[Ellis-van Creveld syndrome](https://sugi.bio/atlas/disease/ellis-van-creveld-syndrome/), [acrofacial dysostosis, Weyers type](https://sugi.bio/atlas/disease/acrofacial-dysostosis-weyers-type/).

**Reported phenotype names (ClinVar):** Ellis-van Creveld syndrome, Curry-Hall syndrome, EVC2-Related Ellis-van Creveld Syndrome, EVC-Related Ellis-van Creveld Syndrome, Chondroectodermal dysplasia, MESOECTODERMAL DYSPLASIA, WEYERS ACRODENTAL DYSOSTOSIS.

## Similar variants {#similar}

Related EVC variant pages (same residue, condition, or type): [EVC p.Pro152Leu](/variant/evc-p-pro152leu), [EVC p.Pro152Ala](/variant/evc-p-pro152ala), [EVC c.1098+1G>A](/variant/evc-c-1098-plus-1g-a), [EVC c.175-2A>G](/variant/evc-c-175-minus-2a-g), [EVC c.1777-1G>A](/variant/evc-c-1777-minus-1g-a), [EVC c.1777-2A>G](/variant/evc-c-1777-minus-2a-g), [EVC c.1886+1G>C](/variant/evc-c-1886-plus-1g-c), [EVC c.1886+5G>A](/variant/evc-c-1886-plus-5g-a).

### 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 1122054). 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.*