# NM_004595.5(SMS):c.665A>T (p.Asp222Val)

https://sugi.bio/variant/sms-p-asp222val

## Summary

**SMS p.Asp222Val (c.665A>T)** is classified **Likely pathogenic** in SMS (ClinVar, Single submitter, 2 submitters; last evaluated 2017-04-20). AlphaMissense: likely pathogenic (0.9989); Absent from gnomAD v4.1.

**At a glance:** Likely pathogenic · review: Single submitter · rsID rs1556001304 · 2 submitters · AlphaMissense likely pathogenic · absent from gnomAD v4.1

## For patients & families {#patients}

This is a change in the SMS gene that is considered likely disease-causing, submitted by 2 submitters.

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

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [SMS](https://sugi.bio/atlas/gene/SMS/) |
| Protein change (HGVS p.) | p.Asp222Val |
| Coding change (HGVS c.) | c.665A>T |
| MANE Select transcript | [NM_004595](https://www.ncbi.nlm.nih.gov/nuccore/NM_004595) |
| dbSNP | [rs1556001304](https://www.ncbi.nlm.nih.gov/snp/rs1556001304/) |
| Variant type | single nucleotide variant |
| Location | chrX:21978881-21978881 (GRCh38) |
| ClinVar | [VCV441113](https://www.ncbi.nlm.nih.gov/clinvar/variation/441113/) |

**All HGVS expressions:** `NC_000023.10:g.21996999A>T`, `NC_000023.11:g.21978881A>T`, `NG_009228.1:g.43158A>T`, `NM_001258423.2:c.506A>T`, `NM_004595.5:c.665A>T`

## Computational & population evidence {#evidence}

**Concordance:** 1 independent predictor **concordant** with the ClinVar classification.

- AlphaMissense **likely pathogenic** (0.9989) — concordant with the pathogenic call
- REVEL 0.977 (strongly pathogenic-leaning) — agrees with AlphaMissense
- SaProt LLR -14.031 (damaging) — agrees with AlphaMissense
- → **In-silico consensus:** AlphaMissense, REVEL and SaProt all call this damaging
- Conservation: phyloP 11.03, GERP 2.2, phastCons 1 — highly conserved (agrees)
- AlphaMissense ranks this among the **top 2%** most-pathogenic-predicted substitutions in SMS (of 2,144 modeled).
- CADD: **PHRED 28.9**. 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 0.34** across the covering region of the MANE Select transcript (21,972,563–21,994,348), spanning 21,785 bp — the region is depleted of missense variation. Chi-square p 3.7e-21. 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: **absent from gnomAD v4.1** — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

*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}

**SMS** population constraint: ClinGen dosage — haploinsufficiency 3, triplosensitivity 0 (0–3 scale). *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):

- **syndromic X-linked intellectual disability Snyder type** — Definitive (XL)

## Protein context {#protein}

Residue **222** lies in the pabs domain.

AlphaFold model confidence (whole protein): pLDDT 95.09, 89% of residues very-high.

**2 experimental structure(s)** (PDB): [3C6K](https://www.rcsb.org/structure/3C6K), [3C6M](https://www.rcsb.org/structure/3C6M).

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

*Describes the biological roles of SMS (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:** SMS's established molecular role includes spermine synthase activity. p.Asp222Val falls in the pabs domain.


### Pathways affected {#pathways}

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

| Pathway (Reactome) | Evidence |
| --- | --- |
| [Metabolism of polyamines](https://reactome.org/content/detail/R-HSA-351202) | curated |

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

**Molecular function:** spermine synthase activity.

## Clinical significance {#significance}

**Likely pathogenic** — review status Single submitter *(criteria provided, single submitter)*, last evaluated 2017-04-20.

**Submitter consensus:** conflicting (1 not provided, 1 Likely pathogenic).

**Submission history:** 2 submissions (2017); classifications have differed over time.

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| GenomeConnect, ClinGen | not provided | no classification provided | phenotyping only |  |
| GeneDx | Likely pathogenic | criteria provided, single submitter | clinical testing | 2017-04-20 |

**Reported phenotype names (ClinVar):** SMS-related disorder, not provided, SMS-related condition, RECLASSIFIED - ADRA2C POLYMORPHISM, RECLASSIFIED - ADRB1 POLYMORPHISM, none provided.

## Similar variants {#similar}

Related SMS variant pages (same residue, condition, or type): [SMS p.Arg234Ter](/variant/sms-p-arg234ter), [SMS p.Gly203Asp](/variant/sms-p-gly203asp), [SMS p.Gly56Ser](/variant/sms-p-gly56ser), [SMS p.Ile196Thr](/variant/sms-p-ile196thr), [SMS p.Pro112Leu](/variant/sms-p-pro112leu), [SMS c.1061+2T>C](/variant/sms-c-1061-plus-2t-c), [SMS c.505+3A>G](/variant/sms-c-505-plus-3a-g), [SMS c.661-4G>A](/variant/sms-c-661-minus-4g-a).

### 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 441113). 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.*