# NM_147127.5(EVC2):c.2305C>T (p.Pro769Ser)

https://sugi.bio/variant/evc2-p-pro769ser

## Summary

**EVC2 p.Pro769Ser (c.2305C>T)** is classified **Uncertain significance** in EVC2 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-07-01). AlphaMissense: likely pathogenic (0.6338); Very rare (popmax 8.47e-05%, nfe); Associated with Ellis-van Creveld syndrome.

**At a glance:** Uncertain significance · review: Multiple submitters · rsID rs1454769055 · 2 submitters · 2 linked conditions · AlphaMissense likely pathogenic · very rare (popmax 8.47e-05%, nfe)

## For patients & families {#patients}

This is a change in the EVC2 gene that is currently of uncertain significance — a definitive interpretation has not yet been established, submitted by 2 submitters, 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 | [EVC2](https://sugi.bio/atlas/gene/EVC2/) |
| Protein change (HGVS p.) | p.Pro769Ser |
| Coding change (HGVS c.) | c.2305C>T |
| MANE Select transcript | [NM_147127](https://www.ncbi.nlm.nih.gov/nuccore/NM_147127) |
| dbSNP | [rs1454769055](https://www.ncbi.nlm.nih.gov/snp/rs1454769055/) |
| Variant type | single nucleotide variant |
| Location | chr4:5622733-5622733 (GRCh38) |
| ClinVar | [VCV958561](https://www.ncbi.nlm.nih.gov/clinvar/variation/958561/) |

**All HGVS expressions:** `NC_000004.11:g.5624460G>A`, `NC_000004.12:g.5622733G>A`, `NG_015821.1:g.91816C>T`, `NM_001166136.2:c.2065C>T`, `NM_147127.5:c.2305C>T`

## Computational & population evidence {#evidence}

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

- AlphaMissense **likely pathogenic** (0.6338)
- REVEL 0.575 (indeterminate)
- SaProt LLR -7.852 (tolerated) — differs from AlphaMissense
- → **In-silico consensus:** AlphaMissense calls this damaging; SaProt does not; REVEL is indeterminate
- Conservation: phyloP 11.431, GERP 2.04, phastCons 1 — highly conserved (agrees)
- AlphaMissense ranks this among the **top 7%** most-pathogenic-predicted substitutions in EVC2 (of 7,595 modeled).
- CADD: **PHRED 24.6**. 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 1.14** across the covering region of the MANE Select transcript (5,562,851–5,708,513), spanning 145,662 bp. Chi-square p 1.9e-08. Describes the region, not this allele; gnomAD v4.1.1's own constrained determination. *Descriptive; no ACMG code 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 EVC2 (1,584 scored positions, the nearest 38 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 **8.47e-05%** (nfe) · 1/1,180,000 in the highest group · 2/1,614,008 alleles overall — very rare (popmax 8.47e-05%, nfe).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| Ashkenazi Jewish (not grpmax-eligible) | 0.00338% | 29,606 |
| European (non-Finnish) (grpmax) | 8.47e-05% | 1,179,999 |

Ashkenazi Jewish shows a higher raw frequency than the grpmax group. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and "Remaining individuals" — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

*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}

**EVC2** population constraint: LOEUF 1.092, pLI 1.7773e-47, missense-Z -1.7856; 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.*

Curated gene–disease validity (ClinGen):

- **acrofacial dysostosis, Weyers type** — Definitive (AD)
- **Ellis-van Creveld syndrome** — Definitive (AR)

## Protein context {#protein}


AlphaFold model confidence (whole protein): pLDDT 73.33, 35% of residues very-high.

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

*Describes the biological roles of EVC2 (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}

EVC2 participates in **2 Reactome pathways** (⚕ = disease pathway):

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

## Clinical significance {#significance}

**Uncertain significance** — review status Multiple submitters *(criteria provided, multiple submitters, no conflicts)*, last evaluated 2025-07-01.

**Submitter consensus:** unanimous (2/2 Uncertain significance).

**Submission history:** 2 submissions (2021–2025); classifications have been stable.

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Labcorp Genetics (formerly Invitae), Labcorp | Uncertain significance | criteria provided, single submitter | clinical testing | 2021-08-31 |
| Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Uncertain significance | criteria provided, single submitter | clinical testing | 2025-07-01 |

## 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, not specified, AllHighlyPenetrant, EVC-Related Ellis-van Creveld Syndrome, EVC2-Related Ellis-van Creveld Syndrome, Chondroectodermal dysplasia, MESOECTODERMAL DYSPLASIA, WEYERS ACRODENTAL DYSOSTOSIS.

## Similar variants {#similar}

Related EVC2 variant pages (same residue, condition, or type): [EVC2 c.2046+1G>A](/variant/evc2-c-2046-plus-1g-a), [EVC2 c.2047-2A>G](/variant/evc2-c-2047-minus-2a-g), [EVC2 c.229-1G>T](/variant/evc2-c-229-minus-1g-t), [EVC2 c.229-2A>G](/variant/evc2-c-229-minus-2a-g), [EVC2 c.3360+1G>A](/variant/evc2-c-3360-plus-1g-a), [EVC2 c.3659+2T>C](/variant/evc2-c-3659-plus-2t-c), [EVC2 c.450+2T>C](/variant/evc2-c-450-plus-2t-c), [EVC2 c.451-2A>G](/variant/evc2-c-451-minus-2a-g).

### 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 958561). 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.*