# NM_001346810.2(DLGAP2):c.2152G>A (p.Gly718Arg)

https://sugi.bio/variant/dlgap2-p-gly718arg

## Summary

**DLGAP2 p.Gly718Arg (c.2152G>A)** is classified **Uncertain significance** in DLGAP2 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-01-04). AlphaMissense: ambiguous (0.5364); Ultra-rare (popmax 0.0134%, amr).

**At a glance:** Uncertain significance · review: Single submitter · rsID rs1012436728 · 1 submitter · AlphaMissense ambiguous · ultra-rare (popmax 0.0134%, amr)

## For patients & families {#patients}

This is a change in the DLGAP2 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 | [DLGAP2](https://sugi.bio/atlas/gene/DLGAP2/) |
| Protein change (HGVS p.) | p.Gly718Arg |
| Coding change (HGVS c.) | c.2152G>A |
| MANE Select transcript | [NM_001346810](https://www.ncbi.nlm.nih.gov/nuccore/NM_001346810) |
| dbSNP | [rs1012436728](https://www.ncbi.nlm.nih.gov/snp/rs1012436728/) |
| Variant type | single nucleotide variant |
| Location | chr8:1668670-1668670 (GRCh38) |
| ClinVar | [VCV3082840](https://www.ncbi.nlm.nih.gov/clinvar/variation/3082840/) |

**All HGVS expressions:** `NC_000008.10:g.1616836G>A`, `NC_000008.11:g.1668670G>A`, `NG_009409.2:g.935952G>A`, `NM_001346810.2:c.2152G>A`

## Computational & population evidence {#evidence}

**Concordance:** AlphaMissense makes no call; REVEL calls this damaging; SaProt does not; AlphaMissense makes no call — descriptive only.

- AlphaMissense **ambiguous** (0.5364) — no call either way
- REVEL 0.673 (pathogenic-leaning)
- SaProt LLR -5.558 (tolerated)
- → **In-silico consensus:** REVEL calls this damaging; SaProt does not; AlphaMissense makes no call
- Conservation: phyloP 9.304, GERP 2.19, phastCons 1 — highly conserved
- ⚠ **Isoform check:** AlphaMissense is numbered on a different transcript (AM **G717R** vs ClinVar **G718R**) — the AlphaMissense read here may be for a different residue; verify against the ClinVar transcript.
- CADD: **PHRED 28.7**. 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.*
- 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 **0.0134%** (amr) · FAF95 0.00627% · FAF99 0.00448% · 7/52,046 in the highest group · 27/1,550,424 alleles overall — ultra-rare (popmax 0.0134%, amr).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| Admixed American (grpmax) | 0.0134% | 7,435 |
| African / African-American | 0.00409% | 24,423 |
| Remaining individuals (not grpmax-eligible) | 0.00334% | 29,950 |
| European (non-Finnish) | 0.00131% | 76,408 |

*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}

**DLGAP2** population constraint: LOEUF 0.425, pLI 0.99993, missense-Z -4.7074; ClinGen dosage — haploinsufficiency 0, 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):

- **complex neurodevelopmental disorder** — Limited (AD)

## Protein context {#protein}


AlphaFold model confidence (whole protein): pLDDT 48.83, 10% of residues very-high.

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

*Describes the biological roles of DLGAP2 (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}

DLGAP2 participates in **1 Reactome pathway** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| [Neurexins and neuroligins](https://reactome.org/content/detail/R-HSA-6794361) | electronic |

## Clinical significance {#significance}

**Uncertain significance** — review status Single submitter *(criteria provided, single submitter)*, last evaluated 2024-01-04.

**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 | 2024-01-04 |

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

## Similar variants {#similar}

Related DLGAP2 variant pages (same residue, condition, or type): [DLGAP2 c.1810+14A>G](/variant/dlgap2-c-1810-plus-14a-g), [DLGAP2 c.2160+19C>G](/variant/dlgap2-c-2160-plus-19c-g), [DLGAP2 p.Glu678=](/variant/dlgap2-p-glu678), [DLGAP2 p.Pro464Gln](/variant/dlgap2-p-pro464gln), [DLGAP2 c.2203-7G>T](/variant/dlgap2-c-2203-minus-7g-t), [DLGAP2 p.Ala1019Gly](/variant/dlgap2-p-ala1019gly), [DLGAP2 p.Ala1026Val](/variant/dlgap2-p-ala1026val), [DLGAP2 p.Ala116Thr](/variant/dlgap2-p-ala116thr).

### 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 3082840). 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.*