# NM_018250.4(INTS9):c.1943G>A (p.Arg648Gln)

https://sugi.bio/variant/ints9-p-arg648gln

## Summary

**INTS9 p.Arg648Gln (c.1943G>A)** is classified **Uncertain significance** in INTS9 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-11-05). AlphaMissense: likely pathogenic (0.6291); Very rare (popmax 0.00458%, nfe).

**At a glance:** Uncertain significance · review: Single submitter · rsID rs747865935 · 1 submitter · AlphaMissense likely pathogenic · very rare (popmax 0.00458%, nfe)

## For patients & families {#patients}

This is a change in the INTS9 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 | [INTS9](https://sugi.bio/atlas/gene/INTS9/) |
| Protein change (HGVS p.) | p.Arg648Gln |
| Coding change (HGVS c.) | c.1943G>A |
| MANE Select transcript | [NM_018250](https://www.ncbi.nlm.nih.gov/nuccore/NM_018250) |
| dbSNP | [rs747865935](https://www.ncbi.nlm.nih.gov/snp/rs747865935/) |
| Variant type | single nucleotide variant |
| Location | chr8:28768180-28768180 (GRCh38) |
| ClinVar | [VCV2366776](https://www.ncbi.nlm.nih.gov/clinvar/variation/2366776/) |

**All HGVS expressions:** `NC_000008.10:g.28625697C>T`, `NC_000008.11:g.28768180C>T`, `NG_016981.2:g.127002G>A`, `NM_001145159.3:c.1880G>A`, `NM_001172562.2:c.1871G>A`, `NM_001363038.2:c.1997G>A`, `NM_018250.4:c.1943G>A`, `NR_026826.3:n.1839G>A`

## Computational & population evidence {#evidence}

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

- AlphaMissense **likely pathogenic** (0.6291)
- REVEL 0.274 (benign-leaning) — differs from AlphaMissense
- SaProt LLR -6.153 (tolerated) — differs from AlphaMissense
- → **In-silico consensus:** AlphaMissense calls this damaging; REVEL and SaProt do not
- Conservation: phyloP 7.591, GERP 1.34, phastCons 1 — highly conserved (agrees)
- CADD: **PHRED 25.4**. 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 0.93** across the covering region of the MANE Select transcript (28,768,149–28,777,917), spanning 9,768 bp. Chi-square p 0.25. Describes the region, not this allele; gnomAD v4.1.1's own constrained determination. *Descriptive; no ACMG code applied.*
- SpliceAI: **not assessed** — this absence is genuinely unknown. Where a position sits between the lowest and the highest record the release holds for its gene, an absent score is a result and we state it as one; this position falls outside them, or the gene has no scored position at all, so that test did not reach here. It may lie outside the scored MANE transcript scope, or it may have been scored with all four deltas below Δ0.2 just past the last surviving record. We cannot tell which, so this claims neither; absence is not evidence against a splicing effect.
- Population frequency (gnomAD v4.1): grpmax **0.00458%** (nfe) · FAF95 0.00358% · FAF99 0.00321% · 54/1,180,052 in the highest group · 60/1,614,024 alleles overall — very rare (popmax 0.00458%, nfe).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| European (non-Finnish) (grpmax) | 0.00458% | 21,853 |
| Remaining individuals (not grpmax-eligible) | 0.0032% | 31,243 |
| East Asian | 0.00223% | 44,894 |
| South Asian | 0.0022% | 45,540 |
| African / African-American | 0.00133% | 74,916 |

*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}

**INTS9** population constraint: LOEUF 0.871, pLI 3.8062e-10, missense-Z 1.6535. *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 **648** lies in an α-helix.

AlphaFold model confidence (whole protein): pLDDT 90.95, 76% of residues very-high.

**15 experimental structure(s)** (PDB): [5V8W](https://www.rcsb.org/structure/5V8W), [7BFP](https://www.rcsb.org/structure/7BFP), [7BFQ](https://www.rcsb.org/structure/7BFQ), [7CUN](https://www.rcsb.org/structure/7CUN), [7PKS](https://www.rcsb.org/structure/7PKS), [7YCX](https://www.rcsb.org/structure/7YCX).

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

*Describes the biological roles of INTS9 (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}

INTS9 participates in **1 Reactome pathway** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| [RNA polymerase II transcribes snRNA genes](https://reactome.org/content/detail/R-HSA-6807505) | other |

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

**Biological process:** snRNA processing, negative regulation of transforming growth factor beta receptor signaling pathway, regulation of transcription elongation by RNA polymerase II, snRNA 3'-end processing, RNA polymerase II transcription initiation surveillance.

## Clinical significance {#significance}

**Uncertain significance** — review status Single submitter *(criteria provided, single submitter)*, last evaluated 2025-11-05.

**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 | 2025-11-05 |

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

## Similar variants {#similar}

Related INTS9 variant pages (same residue, condition, or type): [INTS9 p.Leu417Pro](/variant/ints9-p-leu417pro), [INTS9 p.Ala208Val](/variant/ints9-p-ala208val), [INTS9 p.Ala286Asp](/variant/ints9-p-ala286asp), [INTS9 p.Ala319Val](/variant/ints9-p-ala319val), [INTS9 p.Ala506Thr](/variant/ints9-p-ala506thr), [INTS9 p.Ala560Thr](/variant/ints9-p-ala560thr), [INTS9 p.Arg401Cys](/variant/ints9-p-arg401cys), [INTS9 p.Arg401His](/variant/ints9-p-arg401his).

### Data sources & attribution {#sources}

ClinVar (NCBI — public domain, built 2026-10-14); gnomAD v4.1 (Broad Institute, built 2026-10-15); 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 2366776). 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.*