# NM_001080453.3(INTS1):c.4366T>C (p.Phe1456Leu)

https://sugi.bio/variant/ints1-p-phe1456leu

## Summary

**INTS1 p.Phe1456Leu (c.4366T>C)** is classified **Uncertain significance** in INTS1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-12-27). AlphaMissense: likely pathogenic (0.6825); Very rare (popmax 0.00334%, amr); Associated with Inborn genetic diseases.

**At a glance:** Uncertain significance · review: Single submitter · rsID rs1292681842 · 1 submitter · 1 linked condition · AlphaMissense likely pathogenic · very rare (popmax 0.00334%, amr)

## For patients & families {#patients}

This is a change in the INTS1 gene that is currently of uncertain significance — a definitive interpretation has not yet been established, submitted by 1 submitter, and is linked to Inborn genetic diseases.

*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 | [INTS1](https://sugi.bio/atlas/gene/INTS1/) |
| Protein change (HGVS p.) | p.Phe1456Leu |
| Coding change (HGVS c.) | c.4366T>C |
| MANE Select transcript | [NM_001080453](https://www.ncbi.nlm.nih.gov/nuccore/NM_001080453) |
| dbSNP | [rs1292681842](https://www.ncbi.nlm.nih.gov/snp/rs1292681842/) |
| Variant type | single nucleotide variant |
| Location | chr7:1478849-1478849 (GRCh38) |
| ClinVar | [VCV3110042](https://www.ncbi.nlm.nih.gov/clinvar/variation/3110042/) |

**All HGVS expressions:** `NC_000007.13:g.1518485A>G`, `NC_000007.14:g.1478849A>G`, `NM_001080453.3:c.4366T>C`, `NM_015674.1:c.883T>C`

## Computational & population evidence {#evidence}

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

- AlphaMissense **likely pathogenic** (0.6825)
- REVEL 0.079 (moderately benign-leaning) — differs from AlphaMissense
- SaProt LLR -5.104 (tolerated) — differs from AlphaMissense
- → **In-silico consensus:** AlphaMissense calls this damaging; REVEL and SaProt do not
- SpliceAI predicts **acceptor loss** (Δ 0.23) — a splice-altering prediction on an uncertain variant — a signal for review
- Conservation: phyloP 1.169, GERP -1.47, phastCons 0.071 — weakly conserved position
- CADD: **PHRED 15.47**. 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 1.09** across the covering region of the MANE Select transcript (1,470,580–1,482,592), spanning 12,012 bp. Chi-square p 0.001. Describes the region, not this allele; gnomAD v4.1.1's own constrained determination. *Descriptive; no ACMG code applied.*
- SpliceAI deltas (raw): acceptor loss **0.23**, donor loss **0.00**, acceptor gain **0.01**, donor gain **0.00**. Largest is acceptor loss, 9 bp away.
- SpliceAI deltas (masked): acceptor loss **0.00**, donor loss **0.00**, acceptor gain **0.01**, donor gain **0.00**.
  Masked SpliceAI — what Ensembl VEP and the Broad lookup serve by default — is below the reporting threshold here, so those tools show **no splice signal** for this allele. Masking zeroes a loss scored against a position that is not an annotated splice site, and a gain that merely strengthens an existing one, so the raw score above is describing a cryptic site rather than the site the variant sits on. *No ACMG code is assigned either way.*
- Population frequency (gnomAD v4.1): grpmax **0.00334%** (amr) · FAF95 0.000554% · FAF99 0.000207% · 2/59,902 in the highest group · 5/1,610,498 alleles overall — very rare (popmax 0.00334%, amr).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| Admixed American (grpmax) | 0.00334% | 29,951 |
| East Asian | 0.00223% | 44,822 |
| Remaining individuals (not grpmax-eligible) | 0.0016% | 62,354 |
| European (non-Finnish) | 8.48e-05% | 1,178,586 |

*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}

**INTS1** population constraint: LOEUF 0.785, pLI 2.0443e-30, missense-Z -1.9354. *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 **1456** lies in an α-helix.

AlphaFold model confidence (whole protein): pLDDT 75.49, 15% of residues very-high.

**8 experimental structure(s)** (PDB): [7CUN](https://www.rcsb.org/structure/7CUN), [7PKS](https://www.rcsb.org/structure/7PKS), [7YCX](https://www.rcsb.org/structure/7YCX), [8RBX](https://www.rcsb.org/structure/8RBX), [8RBZ](https://www.rcsb.org/structure/8RBZ), [8RC4](https://www.rcsb.org/structure/8RC4).

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

*Describes the biological roles of INTS1 (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}

INTS1 participates in **1 Reactome pathway** (⚕ = disease pathway):

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

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

**Biological process:** snRNA processing, regulation of transcription elongation by RNA polymerase II, RNA polymerase II transcription initiation surveillance.

## Clinical significance {#significance}

**Uncertain significance** — review status Single submitter *(criteria provided, single submitter)*, last evaluated 2023-12-27.

**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 | 2023-12-27 |

## Associated conditions {#conditions}

[Inborn genetic diseases](https://sugi.bio/atlas/disease/inborn-genetic-diseases/).

**Reported phenotype names (ClinVar):** Inborn genetic diseases.

## Similar variants {#similar}

Related INTS1 variant pages (same residue, condition, or type): [INTS1 c.1283+5G>A](/variant/ints1-c-1283-plus-5g-a), [INTS1 c.2977-5C>T](/variant/ints1-c-2977-minus-5c-t), [INTS1 p.Ala1505Val](/variant/ints1-p-ala1505val), [INTS1 p.Ala1854Val](/variant/ints1-p-ala1854val), [INTS1 p.Ala2155Val](/variant/ints1-p-ala2155val), [INTS1 p.Ala2175Thr](/variant/ints1-p-ala2175thr), [INTS1 p.Ala4Thr](/variant/ints1-p-ala4thr), [INTS1 p.Arg1096Cys](/variant/ints1-p-arg1096cys).

### 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 3110042). 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.*