# NM_014030.4(GIT1):c.405+9G>A

https://sugi.bio/variant/git1-c-405-plus-9g-a

## Summary

**GIT1 c.405+9G>A** is classified **Benign** in GIT1 (ClinVar, Single submitter, 2 submitters; last evaluated 2018-04-26). Rare (popmax 0.257%, amr).

**At a glance:** Benign · review: Single submitter · rsID rs182492370 · 2 submitters · rare (popmax 0.257%, amr)

## For patients & families {#patients}

This is a change in the GIT1 gene that is classified as benign — not considered 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 | [GIT1](https://sugi.bio/atlas/gene/GIT1/) |
| Coding change (HGVS c.) | c.405+9G>A |
| MANE Select transcript | [NM_014030](https://www.ncbi.nlm.nih.gov/nuccore/NM_014030) |
| dbSNP | [rs182492370](https://www.ncbi.nlm.nih.gov/snp/rs182492370/) |
| Variant type | single nucleotide variant |
| Location | chr17:29582689-29582689 (GRCh38) |
| ClinVar | [VCV717636](https://www.ncbi.nlm.nih.gov/clinvar/variation/717636/) |

**All HGVS expressions:** `NC_000017.10:g.27909707C>T`, `NC_000017.11:g.29582689C>T`, `NM_001085454.2:c.405+9G>A`, `NM_014030.4:c.405+9G>A`

## Computational & population evidence {#evidence}

**Concordance:** Mixed / partial computational evidence (see below).

- **Missense predictors (AlphaMissense/REVEL/SaProt) do not apply** to this variant type — they score amino-acid substitutions only. For non-missense variants the computational signal comes from conservation (below), not from a missing predictor score.
- Conservation: phyloP 1.092, GERP 0.587, phastCons 0.916 — weakly conserved position
- CADD: **PHRED 21.2**. 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.*
- Splice region: **near-intronic (+9 nt from the splice site)**.
- SpliceAI: **below the reporting threshold**. This position is scored for a different substitution (C>A, Δ0.56 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 **0.257%** (amr) · FAF95 0.224% · FAF99 0.211% · 154/59,964 in the highest group · 1,927/1,576,608 alleles overall — rare (popmax 0.257%, amr).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| Finnish (not grpmax-eligible) | 1.62% | 62 |
| Admixed American (grpmax) | 0.257% | 389 |
| Remaining individuals (not grpmax-eligible) | 0.093% | 1,075 |
| European (non-Finnish) | 0.0597% | 1,676 |
| African / African-American | 0.00673% | 14,864 |

Finnish shows a higher raw frequency than the grpmax group. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and "Remaining individuals" — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

*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}

**GIT1** population constraint: LOEUF 0.257, pLI 1, missense-Z 3.3718. *Lower LOEUF and higher pLI indicate a gene that tolerates loss-of-function poorly; ClinGen dosage is the curated haploinsufficiency call.*

## Protein context {#protein}


AlphaFold model confidence (whole protein): pLDDT 74.72, 55% of residues very-high.

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

*Describes the biological roles of GIT1 (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:** GIT1's established molecular role includes gamma-tubulin binding.


### Pathways affected {#pathways}

GIT1 participates in **10 Reactome pathways** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| [CDC42 GTPase cycle](https://reactome.org/content/detail/R-HSA-9013148) | curated |
| [RAC1 GTPase cycle](https://reactome.org/content/detail/R-HSA-9013149) | curated |
| [RAC2 GTPase cycle](https://reactome.org/content/detail/R-HSA-9013404) | curated |
| [RAC3 GTPase cycle](https://reactome.org/content/detail/R-HSA-9013423) | curated |
| [RHOJ GTPase cycle](https://reactome.org/content/detail/R-HSA-9013409) | curated |
| [RHOQ GTPase cycle](https://reactome.org/content/detail/R-HSA-9013406) | curated |
| [RHOU GTPase cycle](https://reactome.org/content/detail/R-HSA-9013420) | curated |
| [RHOV GTPase cycle](https://reactome.org/content/detail/R-HSA-9013424) | curated |
| [Activation of RAC1 downstream of NMDARs](https://reactome.org/content/detail/R-HSA-9619229) | electronic |
| [Ephrin signaling](https://reactome.org/content/detail/R-HSA-3928664) | electronic |

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

**Molecular function:** gamma-tubulin binding.

**Biological process:** regulation of cytokinesis, positive regulation of microtubule nucleation.

## Clinical significance {#significance}

**Benign** — review status Single submitter *(criteria provided, single submitter)*, last evaluated 2018-04-26.

**Submitter consensus:** unanimous (2/2 Benign).

**Submission history:** 2 submissions (2018–2019); classifications have been stable.

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Labcorp Genetics (formerly Invitae), Labcorp | Benign | criteria provided, single submitter | clinical testing | 2018-04-26 |
| PreventionGenetics, part of Exact Sciences | Benign | no assertion criteria provided | clinical testing | 2019-08-28 |

**Reported phenotype names (ClinVar):** not provided, GIT1-related disorder, none provided, RECLASSIFIED - ADRA2C POLYMORPHISM, RECLASSIFIED - ADRB1 POLYMORPHISM, GIT1-related condition.

## Similar variants {#similar}

Related GIT1 variant pages (same residue, condition, or type): [GIT1 p.Pro83=](/variant/git1-p-pro83), [GIT1 c.762-205C>T](/variant/git1-c-762-minus-205c-t), [GIT1 p.Ala130Thr](/variant/git1-p-ala130thr), [GIT1 p.Ala183Gly](/variant/git1-p-ala183gly), [GIT1 p.Ala311Val](/variant/git1-p-ala311val), [GIT1 p.Ala402Thr](/variant/git1-p-ala402thr), [GIT1 p.Ala466Val](/variant/git1-p-ala466val), [GIT1 p.Ala488Thr](/variant/git1-p-ala488thr).

### 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 717636). 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.*