# NM_001377540.1(SLMAP):c.1903C>T (p.Arg635Trp)

https://sugi.bio/variant/slmap-p-arg635trp

## Summary

**SLMAP p.Arg635Trp (c.1903C>T)** is classified **Uncertain significance** in SLMAP (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-12-16). AlphaMissense: likely benign (0.1251); Ultra-rare (popmax 0.0156%, eas); Associated with Brugada syndrome.

**At a glance:** Uncertain significance · review: Multiple submitters · 2 submitters · 1 linked condition · AlphaMissense likely benign · ultra-rare (popmax 0.0156%, eas)

## For patients & families {#patients}

This is a change in the SLMAP gene that is currently of uncertain significance — a definitive interpretation has not yet been established, submitted by 2 submitters, and is linked to Brugada 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.*

|  |  |
| --- | --- |
| Typical inheritance (of this condition) | Autosomal dominant, Not applicable |
| Age of onset (of this condition) | Adult, Childhood |
| Prevalence | 1-5 / 10 000 (Europe) |
| Clinical trials | 44 registered for this condition — see ClinicalTrials.gov |

**Commonly reported features of Brugada syndrome** (across patients with this condition; presentation varies — frequencies from Orphanet):

- Syncope — Frequent (79-30%)
- Cardiac arrest — Frequent (79-30%)
- Right bundle branch block — Frequent (79-30%)
- ST segment elevation — Frequent (79-30%)
- Tachycardia — Occasional (29-5%)
- Ventricular fibrillation — Occasional (29-5%)
- Paroxysmal ventricular tachycardia — Occasional (29-5%)
- Supraventricular tachycardia — Occasional (29-5%)

**Support & next steps:** [Condition overview & support (NIH GARD)](https://rarediseases.info.nih.gov/diseases/0001030/index) · [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [SLMAP](https://sugi.bio/atlas/gene/SLMAP/) |
| Protein change (HGVS p.) | p.Arg635Trp |
| Coding change (HGVS c.) | c.1903C>T |
| MANE Select transcript | [NM_001377540](https://www.ncbi.nlm.nih.gov/nuccore/NM_001377540) |
| Variant type | single nucleotide variant |
| Location | chr3:57912584-57912584 (GRCh38) |
| ClinVar | [VCV3709136](https://www.ncbi.nlm.nih.gov/clinvar/variation/3709136/) |

**All HGVS expressions:** `NC_000003.11:g.57898311C>T`, `NC_000003.12:g.57912584C>T`, `NG_042789.1:g.160329C>T`, `NM_001304420.3:c.1852C>T`, `NM_001304421.2:c.1738C>T`, `NM_001304422.3:c.454C>T`, `NM_001304423.3:c.256C>T`, `NM_001311178.2:c.454C>T`, `NM_001311179.2:c.331C>T`, `NM_001377538.1:c.1924C>T`, `NM_001377539.1:c.1903C>T`, `NM_001377540.1:c.1903C>T`, `NM_001377541.1:c.1852C>T`, `NM_001377542.1:c.1852C>T`, `NM_001377545.1:c.1840C>T`, `NM_001377549.1:c.1801C>T`, `NM_001377551.1:c.1789C>T`, `NM_001377552.1:c.1789C>T`, `NM_001377555.1:c.1780C>T`, `NM_001377557.1:c.1738C>T`, `NM_001377559.1:c.1738C>T`, `NM_001377562.1:c.1729C>T`, `NM_001377921.1:c.1729C>T`, `NM_001377922.1:c.1717C>T`, `NM_001377923.1:c.1678C>T`, `NM_001377924.1:c.1666C>T`, `NM_001377925.1:c.1615C>T`, `NM_001377926.1:c.331C>T`, `NM_001377927.1:c.331C>T`, `NM_001377928.1:c.331C>T`, `NM_007159.2:c.1801C>T`, `NM_007159.5:c.1801C>T`, `NR_165328.1:n.2947C>T`

## Computational & population evidence {#evidence}

**Concordance:** ClinVar classifies this **uncertain**; the computational predictors unanimously lean **tolerated** — a triage signal, not a reclassification.

- AlphaMissense **likely benign** (0.1251)
- REVEL 0.174 (moderately benign-leaning) — agrees with AlphaMissense
- SaProt LLR -9.563 (tolerated) — agrees with AlphaMissense
- → **In-silico consensus:** AlphaMissense, REVEL and SaProt all call this tolerated
- Conservation: phyloP 1.524, GERP -0.719, phastCons 1 — weakly conserved position
- ⚠ **Isoform check:** AlphaMissense is numbered on a different transcript (AM **R618W** vs ClinVar **R635W**) — the AlphaMissense read here may be for a different residue; verify against the ClinVar transcript.
- CADD: **PHRED 25.3**. 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 0.85** across the covering region of the MANE Select transcript (57,831,510–57,925,925), spanning 94,415 bp. Chi-square p 9.6e-06. Describes the region, not this allele; gnomAD v4.1.1's own constrained determination. *Descriptive; no ACMG code applied.*
- SpliceAI: **below the reporting threshold**. This position is scored for a different substitution (C>G, Δ0.36 donor gain), so this allele was evaluated and its deltas all fell under Δ0.2 — a prediction of no splicing effect for this allele, not a gap in our data. *No ACMG code assigned.*
- Population frequency (gnomAD v4.1): grpmax **0.0156%** (eas) · FAF95 0.00726% · FAF99 0.00515% · 7/44,868 in the highest group · 11/1,614,042 alleles overall — ultra-rare (popmax 0.0156%, eas).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| East Asian (grpmax) | 0.0156% | 6,410 |
| South Asian | 0.0011% | 91,080 |
| European (non-Finnish) | 0.000254% | 393,323 |

*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}

**SLMAP** population constraint: LOEUF 0.531, pLI 0.85993, missense-Z 2.0271. *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):

- **Brugada syndrome** — Refuted (AD)

## Protein context {#protein}


AlphaFold model confidence (whole protein): pLDDT 77.74, 42% of residues very-high.

**3 experimental structure(s)** (PDB): [6AKM](https://www.rcsb.org/structure/6AKM), [6AR0](https://www.rcsb.org/structure/6AR0), [6AR2](https://www.rcsb.org/structure/6AR2).

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

*Describes the biological roles of SLMAP (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:** SLMAP's established molecular role includes protein-macromolecule adaptor activity.


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

**Molecular function:** protein-macromolecule adaptor activity.

**Biological process:** negative regulation of hippo signaling, protein localization to plasma membrane, regulation of membrane depolarization during cardiac muscle cell action potential, regulation of sodium ion transmembrane transport.

## Clinical significance {#significance}

**Uncertain significance** — review status Multiple submitters *(criteria provided, multiple submitters, no conflicts)*, last evaluated 2025-12-16.

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

**Submission history:** 2 submissions (2024–2025); 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 | 2024-11-27 |
| Ambry Genetics | Uncertain significance | criteria provided, single submitter | clinical testing | 2025-12-16 |

## Associated conditions {#conditions}

[Brugada syndrome](https://sugi.bio/atlas/disease/brugada-syndrome/).

**Reported phenotype names (ClinVar):** Brugada syndrome, not specified, Sudden unexpected nocturnal death syndrome, Sudden Unexplained Death Syndrome, Sudden Unexplained Nocturnal Death Syndrome (SUNDS), Sudden unexplained nocturnal death syndrome, AllHighlyPenetrant.

## Similar variants {#similar}

Related SLMAP variant pages (same residue, condition, or type): [SLMAP p.Arg635Gln](/variant/slmap-p-arg635gln), [SLMAP c.*38C>T](/variant/slmap-c-star-38c-t), [SLMAP c.*55G>A](/variant/slmap-c-star-55g-a), [SLMAP c.*70G>A](/variant/slmap-c-star-70g-a), [SLMAP p.Ala365Asp](/variant/slmap-p-ala365asp), [SLMAP p.Ala506Ser](/variant/slmap-p-ala506ser), [SLMAP p.Ala597Val](/variant/slmap-p-ala597val), [SLMAP p.Arg136Gln](/variant/slmap-p-arg136gln).

### 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 3709136). 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.*