# NM_002998.4(SDC2):c.448A>G (p.Ile150Val)

https://sugi.bio/variant/sdc2-p-ile150val

## Summary

**SDC2 p.Ile150Val (c.448A>G)** is classified **Uncertain significance** in SDC2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-09-05). AlphaMissense: likely benign (0.2386); Very rare (popmax 0.00134%, afr).

**At a glance:** Uncertain significance · review: Single submitter · 1 submitter · AlphaMissense likely benign · very rare (popmax 0.00134%, afr)

## For patients & families {#patients}

This is a change in the SDC2 gene that is currently of uncertain significance — a definitive interpretation has not yet been established, submitted by 1 submitter.

*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 | [SDC2](https://sugi.bio/atlas/gene/SDC2/) |
| Protein change (HGVS p.) | p.Ile150Val |
| Coding change (HGVS c.) | c.448A>G |
| MANE Select transcript | [NM_002998](https://www.ncbi.nlm.nih.gov/nuccore/NM_002998) |
| Variant type | single nucleotide variant |
| Location | chr8:96609390-96609390 (GRCh38) |
| ClinVar | [VCV4161090](https://www.ncbi.nlm.nih.gov/clinvar/variation/4161090/) |

**All HGVS expressions:** `NC_000008.10:g.97621618A>G`, `NC_000008.11:g.96609390A>G`, `NM_002998.4:c.448A>G`

## Computational & population evidence {#evidence}

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

- AlphaMissense **likely benign** (0.2386)
- REVEL 0.301 (indeterminate)
- SaProt LLR -9.672 (tolerated) — agrees with AlphaMissense
- → **In-silico consensus:** AlphaMissense and SaProt both call this tolerated; REVEL makes no call
- Conservation: phyloP 9.398, GERP 1.92, phastCons 1 — highly conserved (differs from AlphaMissense)
- CADD: **PHRED 24.7**. 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 0.95** across the covering region of the MANE Select transcript (96,494,272–96,609,545), spanning 115,273 bp. Chi-square p 0.45. 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 **0.00134%** (afr) · 1/74,750 in the highest group · 1/1,610,350 alleles overall — very rare (popmax 0.00134%, afr).

*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}

**SDC2** population constraint: LOEUF 1.167, pLI 0.0014725, missense-Z 0.362. *Lower LOEUF and higher pLI indicate a gene that tolerates loss-of-function poorly; ClinGen dosage is the curated haploinsufficiency call.*

## Protein context {#protein}

Residue **150** lies in an α-helix.

AlphaFold model confidence (whole protein): pLDDT 60.79, 8% of residues very-high.

**1 experimental structure(s)** (PDB): [6ITH](https://www.rcsb.org/structure/6ITH).

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

*Describes the biological roles of SDC2 (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:** SDC2's established molecular role includes PDZ domain binding. In Reactome, SDC2 is annotated in disease pathway(s) including **Attachment and Entry**, **Defective B3GALT6 causes EDSP2 and SEMDJL1**.

**Disease mechanism (Reactome):** SDC2 loss or alteration is curated in [Attachment and Entry](https://reactome.org/content/detail/R-HSA-9694614), [Defective B3GALT6 causes EDSP2 and SEMDJL1](https://reactome.org/content/detail/R-HSA-4420332), [Defective B3GAT3 causes JDSSDHD](https://reactome.org/content/detail/R-HSA-3560801).

### Pathways affected {#pathways}

SDC2 participates in **21 Reactome pathways** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| ⚕ [Attachment and Entry](https://reactome.org/content/detail/R-HSA-9694614) | other |
| ⚕ [Defective B3GALT6 causes EDSP2 and SEMDJL1](https://reactome.org/content/detail/R-HSA-4420332) | other |
| ⚕ [Defective B3GAT3 causes JDSSDHD](https://reactome.org/content/detail/R-HSA-3560801) | other |
| ⚕ [Defective B4GALT7 causes EDS, progeroid type](https://reactome.org/content/detail/R-HSA-3560783) | other |
| ⚕ [Defective EXT1 causes exostoses 1, TRPS2 and CHDS](https://reactome.org/content/detail/R-HSA-3656253) | other |
| ⚕ [Defective EXT2 causes exostoses 2](https://reactome.org/content/detail/R-HSA-3656237) | other |
| ⚕ [Dengue Virus Attachment and Entry](https://reactome.org/content/detail/R-HSA-9918485) | other |
| ⚕ [Dengue Virus-Host Interactions](https://reactome.org/content/detail/R-HSA-9918481) | other |
| ⚕ [RSV-host interactions](https://reactome.org/content/detail/R-HSA-9833110) | other |
| ⚕ [Respiratory syncytial virus (RSV) attachment and entry](https://reactome.org/content/detail/R-HSA-9820960) | other |
| [Initiation of coagulation cascade](https://reactome.org/content/detail/R-HSA-9769735) | curated |
| [Regulation of clotting cascade](https://reactome.org/content/detail/R-HSA-9769739) | curated |
| [Cell surface interactions at the vascular wall](https://reactome.org/content/detail/R-HSA-202733) | other |
| [EPHB-mediated forward signaling](https://reactome.org/content/detail/R-HSA-3928662) | other |
| [Glycosaminoglycan-protein linkage region biosynthesis](https://reactome.org/content/detail/R-HSA-1971475) | other |
| [HS-GAG biosynthesis](https://reactome.org/content/detail/R-HSA-2022928) | other |
| [HS-GAG degradation](https://reactome.org/content/detail/R-HSA-2024096) | other |
| [Post-translational protein phosphorylation](https://reactome.org/content/detail/R-HSA-8957275) | other |
| [Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs)](https://reactome.org/content/detail/R-HSA-381426) | other |
| [Retinoid metabolism and transport](https://reactome.org/content/detail/R-HSA-975634) | other |
| [Syndecan interactions](https://reactome.org/content/detail/R-HSA-3000170) | other |

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

**Molecular function:** PDZ domain binding, identical protein binding.

## Clinical significance {#significance}

**Uncertain significance** — review status Single submitter *(criteria provided, single submitter)*, last evaluated 2025-09-05.

**Submitter consensus:** unanimous (1/1 Uncertain significance).

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Ambry Genetics | Uncertain significance | criteria provided, single submitter | clinical testing | 2025-09-05 |

**Reported phenotype names (ClinVar):** not specified, AllHighlyPenetrant.

## Similar variants {#similar}

Related SDC2 variant pages (same residue, condition, or type): [SDC2 p.Ile150Thr](/variant/sdc2-p-ile150thr), [SDC2 p.Ser71Thr](/variant/sdc2-p-ser71thr), [SDC2 p.Ala124Gly](/variant/sdc2-p-ala124gly), [SDC2 p.Ala14Val](/variant/sdc2-p-ala14val), [SDC2 p.Arg170Cys](/variant/sdc2-p-arg170cys), [SDC2 p.Arg170His](/variant/sdc2-p-arg170his), [SDC2 p.Arg184His](/variant/sdc2-p-arg184his), [SDC2 p.Arg72Gln](/variant/sdc2-p-arg72gln).

### Data sources & attribution {#sources}

ClinVar (NCBI — public domain, built 2026-10-14); 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 2026-10-14); 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 4161090). 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.*