# NM_006421.5(ARFGEF1):c.4987G>A (p.Val1663Ile)

https://sugi.bio/variant/arfgef1-p-val1663ile

## Summary

**ARFGEF1 p.Val1663Ile (c.4987G>A)** is classified **Uncertain significance** in ARFGEF1 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-06-17). AlphaMissense: likely benign (0.0828); Very rare (popmax 0.00439%, sas); Associated with developmental delay, impaired speech, and behavioral abnormalities, with or without seizures.

**At a glance:** Uncertain significance · review: Multiple submitters · 2 submitters · 1 linked condition · AlphaMissense likely benign · very rare (popmax 0.00439%, sas)

## For patients & families {#patients}

This is a change in the ARFGEF1 gene that is currently of uncertain significance — a definitive interpretation has not yet been established, submitted by 2 submitters, and is linked to developmental delay, impaired speech, and behavioral abnormalities, with or without seizures.

*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 | [ARFGEF1](https://sugi.bio/atlas/gene/ARFGEF1/) |
| Protein change (HGVS p.) | p.Val1663Ile |
| Coding change (HGVS c.) | c.4987G>A |
| MANE Select transcript | [NM_006421](https://www.ncbi.nlm.nih.gov/nuccore/NM_006421) |
| Variant type | single nucleotide variant |
| Location | chr8:67203224-67203224 (GRCh38) |
| ClinVar | [VCV4078007](https://www.ncbi.nlm.nih.gov/clinvar/variation/4078007/) |

**All HGVS expressions:** `NC_000008.10:g.68115459C>T`, `NC_000008.11:g.67203224C>T`, `NM_001413184.1:c.4987G>A`, `NM_001413185.1:c.4969G>A`, `NM_001413186.1:c.4969G>A`, `NM_001413187.1:c.4987G>A`, `NM_001413188.1:c.4387G>A`, `NM_001413189.1:c.4969G>A`, `NM_001413190.1:c.4981G>A`, `NM_001413191.1:c.4891G>A`, `NM_001413192.1:c.4873G>A`, `NM_001413193.1:c.4369G>A`, `NM_001413194.1:c.4987G>A`, `NM_001413196.1:c.3562G>A`, `NM_001413197.1:c.4387G>A`, `NM_006421.5:c.4987G>A`, `NR_182117.1:n.5428G>A`

## Computational & population evidence {#evidence}

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

- AlphaMissense **likely benign** (0.0828)
- REVEL 0.059 (moderately benign-leaning) — agrees with AlphaMissense
- SaProt LLR -6.753 (tolerated) — agrees with AlphaMissense
- → **In-silico consensus:** AlphaMissense, REVEL and SaProt all call this tolerated
- Conservation: phyloP 3.381, GERP -0.161, phastCons 1 — highly conserved (differs from AlphaMissense)
- CADD: **PHRED 22.6**. 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 0.57** across the covering region of the MANE Select transcript (67,198,937–67,204,816), spanning 5,879 bp. Chi-square p 2.1e-13. 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 **0.00439%** (sas) · FAF95 0.00143% · FAF99 0.000891% · 4/91,076 in the highest group · 6/1,461,820 alleles overall — very rare (popmax 0.00439%, sas).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| South Asian (grpmax) | 0.00439% | 22,769 |
| European (non-Finnish) | 0.000169% | 589,995 |

*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}

**ARFGEF1** population constraint: LOEUF 0.236, pLI 1, missense-Z 6.96. *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):

- **developmental delay, impaired speech, and behavioral abnormalities, with or without seizures** — Definitive (AD)

## Protein context {#protein}

Residue **1663** lies in a UniProt-annotated variant site (in dedisb; decreased protein abundance); a UniProt-annotated variant site (in dedisb).

AlphaFold model confidence (whole protein): pLDDT 76.23, 42% of residues very-high.

**3 experimental structure(s)** (PDB): [3LTL](https://www.rcsb.org/structure/3LTL), [5EE5](https://www.rcsb.org/structure/5EE5), [5J5C](https://www.rcsb.org/structure/5J5C).

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

*Describes the biological roles of ARFGEF1 (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:** ARFGEF1's established molecular role includes guanyl-nucleotide exchange factor activity.


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

**Molecular function:** guanyl-nucleotide exchange factor activity, myosin binding, protein kinase A regulatory subunit binding.

**Biological process:** Golgi organization, glycoprotein biosynthetic process, endomembrane system organization, negative regulation of actin filament polymerization, negative regulation of GTPase activity, positive regulation of wound healing.

## Clinical significance {#significance}

**Uncertain significance** — review status Multiple submitters *(criteria provided, multiple submitters, no conflicts)*, last evaluated 2025-06-17.

**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 |
| --- | --- | --- | --- | --- |
| Revvity Omics, Revvity | Uncertain significance | criteria provided, single submitter | clinical testing | 2024-05-20 |
| Dasa | Uncertain significance | criteria provided, single submitter | clinical testing | 2025-06-17 |

## Associated conditions {#conditions}

[developmental delay, impaired speech, and behavioral abnormalities, with or without seizures](https://sugi.bio/atlas/disease/developmental-delay-impaired-speech-and-behavioral-abnormalities-with-or-without-seizures/).

**Reported phenotype names (ClinVar):** Developmental delay, impaired speech, and behavioral abnormalities, with or without seizures.

## Similar variants {#similar}

Related ARFGEF1 variant pages (same residue, condition, or type): [ARFGEF1 p.Arg1272Ter](/variant/arfgef1-p-arg1272ter), [ARFGEF1 p.Arg1543Ter](/variant/arfgef1-p-arg1543ter), [ARFGEF1 p.Arg1774Ter](/variant/arfgef1-p-arg1774ter), [ARFGEF1 p.Asp798Asn](/variant/arfgef1-p-asp798asn), [ARFGEF1 c.2699-3C>T](/variant/arfgef1-c-2699-minus-3c-t), [ARFGEF1 p.Asn373Ser](/variant/arfgef1-p-asn373ser), [ARFGEF1 p.Ile481Leu](/variant/arfgef1-p-ile481leu), [ARFGEF1 p.Phe1796Leu](/variant/arfgef1-p-phe1796leu).

### 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 4078007). 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.*