Is INTS11 p.Ala466Val (c.1397C>T) pathogenic?

INTS11 p.Ala466Val (c.1397C>T) is classified Uncertain significance in INTS11 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-03). AlphaMissense: likely benign (0.0798); Rare (popmax 0.105%, afr).

How common is INTS11 p.Ala466Val (c.1397C>T) in the general population?

INTS11 p.Ala466Val (c.1397C>T) is rare (popmax 0.105%, afr) (gnomAD).

What do computational predictors say about INTS11 p.Ala466Val (c.1397C>T)?

AlphaMissense predicts likely benign (score 0.0798) — an in-silico prediction, not a clinical call.

INTS11 p.Ala466Val

c.1397C>T · VCV4275909

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0798 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.105%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0798	likely benign
REVEL	0.054	moderately benign-leaning
SaProt	LLR -7.61	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 3.3	GERP -2.4, phastCons 1
Regional constraint	o/e 1.06	unconstrained · MANE · 13 kb · p 0.087 · regional, not allelic
Overall
CADD	20.4	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.105% African / African-American · 78/74,106 alleles

Filtering AF 0.0864% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0795%

Overall 0.00744% 117/1,572,678 alleles · rare exomes 68/1,420,408 · genomes 49/152,270 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.105%	950
Middle Eastern	0.017%	5,868
South Asian	0.0162%	6,189
Admixed American	0.0106%	9,469
Remaining individualsnot grpmax-eligible	0.00661%	15,139
European (non-Finnish)	0.00121%	82,493

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: INTS11
Protein: p.Ala466Val
Coding: c.1397C>T
MANE Select: NM_017871
Type: single nucleotide variant
Location: chr1:1312598 (GRCh38)
Gene constraint: LOEUF 1.223 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 90.82 · 15 PDB
Residue 466: an α-helix

Full INTS11 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

INTS11 p.Ala466Thr Uncertain significance ★ ⚠ same residue
INTS11 c.28+1406C>T Uncertain significance ★★ same type
INTS11 p.Ala241Thr Uncertain significance ★★ ⚠ same type
INTS11 p.Arg231Cys Uncertain significance ★★ ⚠ same type
INTS11 p.Gln467His Uncertain significance ★★ ⚠ same type
INTS11 p.Glu227Lys Uncertain significance ★★ same type
INTS11 p.His157Arg Uncertain significance ★★ ⚠ same type
INTS11 c.1607+18C>A Benign ★★ same type

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/ints11-p-ala466val (accessed [today's date]).

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