# NM_005045.4(RELN):c.2086T>C (p.Ser696Pro)

https://sugi.bio/variant/reln-p-ser696pro

## Summary

**RELN p.Ser696Pro (c.2086T>C)** is classified **Conflicting classifications of pathogenicity** in RELN (ClinVar, Conflicting submitters, 2 submitters; last evaluated 2025-09-07). AlphaMissense: likely pathogenic (0.959); Ultra-rare (popmax 0.01%, amr); Associated with familial temporal lobe epilepsy 7.

**At a glance:** Conflicting classifications of pathogenicity · review: Conflicting submitters · rsID rs765274194 · 2 submitters · 2 linked conditions · AlphaMissense likely pathogenic · ultra-rare (popmax 0.01%, amr)

## For patients & families {#patients}

This is a change in the RELN gene that is of uncertain or conflicting significance (submitters disagree on it), submitted by 2 submitters, and is linked to familial temporal lobe epilepsy 7.

*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.*

|  |  |
| --- | --- |
| Diagnostic panels | RELN is a diagnostic-grade gene on 13 Genomics England panels |

**Support & next steps:** [Condition overview & support (NIH GARD)](https://rarediseases.info.nih.gov/diseases/0016112/index) · [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [RELN](https://sugi.bio/atlas/gene/RELN/) |
| Protein change (HGVS p.) | p.Ser696Pro |
| Coding change (HGVS c.) | c.2086T>C |
| MANE Select transcript | [NM_005045](https://www.ncbi.nlm.nih.gov/nuccore/NM_005045) |
| dbSNP | [rs765274194](https://www.ncbi.nlm.nih.gov/snp/rs765274194/) |
| Variant type | single nucleotide variant |
| Location | chr7:103636452-103636452 (GRCh38) |
| ClinVar | [VCV287543](https://www.ncbi.nlm.nih.gov/clinvar/variation/287543/) |

**All HGVS expressions:** `NC_000007.13:g.103276899A>G`, `NC_000007.14:g.103636452A>G`, `NG_011877.2:g.358065T>C`, `NM_005045.4:c.2086T>C`, `NM_173054.3:c.2086T>C`

## Computational & population evidence {#evidence}

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

- AlphaMissense **likely pathogenic** (0.959)
- REVEL 0.271 (benign-leaning) — differs from AlphaMissense
- → **In-silico consensus:** AlphaMissense calls this damaging; REVEL does not; SaProt makes no call
- Conservation: phyloP 11.216, GERP 1.82, phastCons 1 — highly conserved (agrees)
- **SaProt:** not scored — SaProt is structure-aware and AlphaFold DB has no model for this protein. That is a property of the dataset, not of the variant, and is not evidence either way.
- CADD: **PHRED 28.2**. 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 (103,557,010–103,989,356), spanning 432,346 bp. Chi-square p 0.0016. 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 RELN (3,598 scored positions, the nearest 17 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 **0.01%** (amr) · FAF95 0.00428% · FAF99 0.00295% · 6/59,976 in the highest group · 6/1,612,176 alleles overall — ultra-rare (popmax 0.01%, amr).

*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}

**RELN** population constraint: LOEUF 0.276, pLI 1, missense-Z 4.2857; ClinGen dosage — haploinsufficiency 0/3, 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):

- **lissencephaly with cerebellar hypoplasia** — Definitive (AR)
- **complex neurodevelopmental disorder** — Disputed (AD)

## Protein context {#protein}

Residue **696** lies in the egf-like 1 domain.

**1 experimental structure(s)** (PDB): [8G21](https://www.rcsb.org/structure/8G21).

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

*Describes the biological roles of RELN (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}

RELN participates in **1 Reactome pathway** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| [Reelin signalling pathway](https://reactome.org/content/detail/R-HSA-8866376) | other |

## Clinical significance {#significance}

**Conflicting classifications of pathogenicity** — review status Conflicting submitters *(criteria provided, conflicting classifications)*, last evaluated 2025-09-07.

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

**Submission history:** 2 submissions (2016–2025); classifications have differed over time.

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Eurofins Ntd Llc (ga) | Uncertain significance | criteria provided, single submitter | clinical testing | 2016-05-12 |
| Labcorp Genetics (formerly Invitae), Labcorp | Likely benign | criteria provided, single submitter | clinical testing | 2025-09-07 |

## Associated conditions {#conditions}

[familial temporal lobe epilepsy 7](https://sugi.bio/atlas/disease/familial-temporal-lobe-epilepsy-7/), [Norman-Roberts syndrome](https://sugi.bio/atlas/disease/norman-roberts-syndrome/).

**Reported phenotype names (ClinVar):** Familial temporal lobe epilepsy 7, not provided, Norman-Roberts syndrome, Lissencephaly 2 (Norman-Roberts type), none provided.

## Same-residue context {#hotspot}

Residue **696** carries **1 other pathogenic ClinVar variant** — a recurrently-mutated position: [RELN p.Ser696fs](/variant/reln-p-ser696fs). *Positional co-occurrence of independent ClinVar records, not functional proof.*

## Similar variants {#similar}

Related RELN variant pages (same residue, condition, or type): [RELN p.Ser696fs](/variant/reln-p-ser696fs), [RELN c.3912+2T>G](/variant/reln-c-3912-plus-2t-g), [RELN c.7349+2T>C](/variant/reln-c-7349-plus-2t-c), [RELN p.Arg1622Ter](/variant/reln-p-arg1622ter), [RELN c.1893-3C>T](/variant/reln-c-1893-minus-3c-t), [RELN c.227-3C>T](/variant/reln-c-227-minus-3c-t), [RELN c.2465+5G>T](/variant/reln-c-2465-plus-5g-t), [RELN c.6072+3A>G](/variant/reln-c-6072-plus-3a-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 287543). 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.*