Is INTS1 p.Phe1456Leu (c.4366T>C) pathogenic?

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.

What condition is associated with INTS1 p.Phe1456Leu (c.4366T>C)?

INTS1 p.Phe1456Leu (c.4366T>C) is associated with Inborn genetic diseases (ClinVar).

How common is INTS1 p.Phe1456Leu (c.4366T>C) in the general population?

INTS1 p.Phe1456Leu (c.4366T>C) is very rare (popmax 0.00334%, amr) (gnomAD).

What do computational predictors say about INTS1 p.Phe1456Leu (c.4366T>C)?

AlphaMissense predicts likely pathogenic (score 0.6825) — an in-silico prediction, not a clinical call.

INTS1 p.Phe1456Leu

c.4366T>C · rs1292681842 · VCV3110042

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.6825 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00334%, amr)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.6825	likely pathogenic
REVEL	0.079	moderately benign-leaning
SaProt	LLR -5.10	tolerated
⇒ AlphaMissense calls this damaging; REVEL and SaProt do not.
Splicing
SpliceAI	Δ0.23	acceptor loss, 9 bp away · masked 0 · deltas
Constraint at this position
Conservation	phyloP 1.2	GERP -1.5, phastCons 0.071
Regional constraint	o/e 1.09	unconstrained · MANE · 12 kb · p 0.001 · regional, not allelic
Overall
CADD	15.47	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00334% Admixed American · 2/59,902 alleles

Filtering AF 0.000554% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000207%

Overall 0.00031% 5/1,610,498 alleles · very rare exomes 3/1,458,228 · genomes 2/152,270 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00334%	29,951
East Asian	0.00223%	44,822
Remaining individualsnot grpmax-eligible	0.0016%	62,354
European (non-Finnish)	8.48e-05%	1,178,586

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: INTS1
Protein: p.Phe1456Leu
Coding: c.4366T>C
MANE Select: NM_001080453
dbSNP: rs1292681842
Type: single nucleotide variant
Location: chr7:1478849 (GRCh38)
Gene constraint: LOEUF 0.785 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 75.49 · 8 PDB
Residue 1456: an α-helix

Full INTS1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

INTS1 c.1283+5G>A Uncertain significance ★★ same condition
INTS1 c.2977-5C>T Uncertain significance ★★ same condition
INTS1 p.Ala1505Val Uncertain significance ★★ ⚠ same condition
INTS1 p.Ala1854Val Uncertain significance ★★ ⚠ same condition
INTS1 p.Ala2155Val Uncertain significance ★★ ⚠ same condition
INTS1 p.Ala2175Thr Uncertain significance ★★ ⚠ same condition
INTS1 p.Ala4Thr Uncertain significance ★★ ⚠ same condition
INTS1 p.Arg1096Cys Uncertain significance ★★ ⚠ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/ints1-p-phe1456leu (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown