Is INTS1 p.Ala1886Val (c.5657C>T) pathogenic?

INTS1 p.Ala1886Val (c.5657C>T) is classified Uncertain significance in INTS1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-05-19). AlphaMissense: ambiguous (0.5131); Ultra-rare (popmax 0.042%, amr); Associated with Inborn genetic diseases.

What condition is associated with INTS1 p.Ala1886Val (c.5657C>T)?

INTS1 p.Ala1886Val (c.5657C>T) is associated with Inborn genetic diseases (ClinVar).

How common is INTS1 p.Ala1886Val (c.5657C>T) in the general population?

INTS1 p.Ala1886Val (c.5657C>T) is ultra-rare (popmax 0.042%, amr) (gnomAD).

What do computational predictors say about INTS1 p.Ala1886Val (c.5657C>T)?

AlphaMissense predicts ambiguous (score 0.5131) — an in-silico prediction, not a clinical call.

INTS1 p.Ala1886Val

c.5657C>T · VCV4038935

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.5131 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.042%, amr)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.5131	ambiguous
REVEL	0.336	indeterminate
SaProt	LLR -7.98	tolerated
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 1.4, phastCons 1
Regional constraint	o/e 1.09	unconstrained · MANE · 12 kb · p 0.001 · regional, not allelic
Overall
CADD	23.4	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 0.042% Admixed American · 25/59,554 alleles

Filtering AF 0.0291% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0249%

Overall 0.00269% 43/1,601,376 alleles · ultra-rare exomes 22/1,449,170 · genomes 21/152,206 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.042%	2,382
African / African-American	0.0134%	7,442
European (non-Finnish)	0.00068%	146,967

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.Ala1886Val
Coding: c.5657C>T
MANE Select: NM_001080453
Type: single nucleotide variant
Location: chr7:1474340 (GRCh38)
Gene constraint: LOEUF 0.785 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 75.49 · 8 PDB
Residue 1886: an α-helix; a UniProt-annotated variant site (in ndcagf; decreased protein abundance)

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-ala1886val (accessed [today's date]).

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