# NM_014704.4(CEP104):c.1966C>T (p.Arg656Cys)

https://sugi.bio/variant/cep104-p-arg656cys

## Summary

**CEP104 p.Arg656Cys (c.1966C>T)** is classified **Benign/Likely benign** in CEP104 (ClinVar, Multiple submitters, 8 submitters; last evaluated 2026-06-01). AlphaMissense: likely benign (0.2247); Rare (popmax 0.508%, nfe); Associated with Joubert syndrome 25.

**At a glance:** Benign/Likely benign · review: Multiple submitters · rsID rs148465057 · 8 submitters · 1 linked condition · AlphaMissense likely benign · rare (popmax 0.508%, nfe)

## For patients & families {#patients}

This is a change in the CEP104 gene that is classified as benign/likely benign — not considered disease-causing, submitted by 8 submitters, and is linked to Joubert syndrome 25.

*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/0016159/index) · [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [CEP104](https://sugi.bio/atlas/gene/CEP104/) |
| Protein change (HGVS p.) | p.Arg656Cys |
| Coding change (HGVS c.) | c.1966C>T |
| MANE Select transcript | [NM_014704](https://www.ncbi.nlm.nih.gov/nuccore/NM_014704) |
| dbSNP | [rs148465057](https://www.ncbi.nlm.nih.gov/snp/rs148465057/) |
| Variant type | single nucleotide variant |
| Location | chr1:3829868-3829868 (GRCh38) |
| ClinVar | [VCV707355](https://www.ncbi.nlm.nih.gov/clinvar/variation/707355/) |

**All HGVS expressions:** `NC_000001.10:g.3746432G>A`, `NC_000001.11:g.3829868G>A`, `NG_046726.1:g.32366C>T`, `NM_014704.4:c.1966C>T`

## Computational & population evidence {#evidence}

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

- AlphaMissense **likely benign** (0.2247)
- REVEL 0.409 (indeterminate)
- SaProt LLR -13.28 (damaging) — differs from AlphaMissense
- → **In-silico consensus:** SaProt calls this damaging; AlphaMissense does not; REVEL makes no call
- Conservation: phyloP 11.496, GERP 1.98, phastCons 1 — highly conserved (differs from AlphaMissense)
- CADD: **PHRED 32.0**. 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 0.91** across the covering region of the MANE Select transcript (3,815,405–3,852,407), spanning 37,002 bp. Chi-square p 0.0023. 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 **0.508%** (nfe) · FAF95 0.497% · FAF99 0.492% · 5,989/1,180,008 in the highest group · 6,579/1,614,086 alleles overall — rare (popmax 0.508%, nfe).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| European (non-Finnish) (grpmax) | 0.508% | 197 |
| Remaining individuals (not grpmax-eligible) | 0.336% | 298 |
| Middle Eastern | 0.148% | 674 |
| South Asian | 0.148% | 675 |
| Finnish (not grpmax-eligible) | 0.119% | 842 |
| Amish (not grpmax-eligible) | 0.11% | 912 |
| Admixed American | 0.105% | 953 |
| African / African-American | 0.0933% | 1,072 |
| East Asian | 0.0379% | 2,640 |
| Ashkenazi Jewish (not grpmax-eligible) | 0.0304% | 3,289 |

*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}

**CEP104** population constraint: LOEUF 0.851, pLI 2.4722e-17, missense-Z 1.5089. *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):

- **ciliopathy** — Definitive (AR)

## Protein context {#protein}

Residue **656** lies in a UniProt-annotated variant site (in mrt77); an α-helix.

AlphaFold model confidence (whole protein): pLDDT 76.75, 51% of residues very-high.

**2 experimental structure(s)** (PDB): [5LPH](https://www.rcsb.org/structure/5LPH), [5LPI](https://www.rcsb.org/structure/5LPI).

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

*Describes the biological roles of CEP104 (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:** CEP104's established molecular role includes identical protein binding.


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

**Molecular function:** identical protein binding.

## Clinical significance {#significance}

**Benign/Likely benign** — review status Multiple submitters *(criteria provided, multiple submitters, no conflicts)*, last evaluated 2026-06-01.

**Submitter consensus:** conflicting (7 Likely benign, 1 Benign).

**Submission history:** 8 submissions (2019–2026); classifications have differed over time.

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) | Likely benign | no assertion criteria provided | clinical testing |  |
| Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | Likely benign | no assertion criteria provided | clinical testing |  |
| GeneDx | Likely benign | criteria provided, single submitter | clinical testing | 2019-10-23 |
| Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | Likely benign | no assertion criteria provided | clinical testing |  |
| Breakthrough Genomics, Breakthrough Genomics | Likely benign | criteria provided, single submitter | not provided |  |
| Labcorp Genetics (formerly Invitae), Labcorp | Benign | criteria provided, single submitter | clinical testing | 2026-02-04 |
| CeGaT Center for Human Genetics Tuebingen | Likely benign | criteria provided, single submitter | clinical testing | 2026-06-01 |
| Blueprint Genetics | Likely benign | criteria provided, single submitter | clinical testing | 2024-11-20 |

## Associated conditions {#conditions}

[Joubert syndrome 25](https://sugi.bio/atlas/disease/joubert-syndrome-25/).

**Reported phenotype names (ClinVar):** Joubert syndrome 25, not provided, not specified, none provided, AllHighlyPenetrant.

## Similar variants {#similar}

Related CEP104 variant pages (same residue, condition, or type): [CEP104 p.Arg299Ter](/variant/cep104-p-arg299ter), [CEP104 p.Arg55Ter](/variant/cep104-p-arg55ter), [CEP104 p.Glu627Ter](/variant/cep104-p-glu627ter), [CEP104 p.Lys270Ter](/variant/cep104-p-lys270ter), [CEP104 p.Tyr253Ter](/variant/cep104-p-tyr253ter), [CEP104 c.1120-5T>A](/variant/cep104-c-1120-minus-5t-a), [CEP104 p.Ala269Thr](/variant/cep104-p-ala269thr), [CEP104 p.Ala28Val](/variant/cep104-p-ala28val).

### 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 707355). 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.*