Is INTS1 p.Ala2155Val (c.6464C>T) pathogenic?

INTS1 p.Ala2155Val (c.6464C>T) is classified Uncertain significance in INTS1 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-04-03). AlphaMissense: likely benign (0.2807); Ultra-rare (popmax 0.0284%, eas); Associated with Inborn genetic diseases.

What condition is associated with INTS1 p.Ala2155Val (c.6464C>T)?

INTS1 p.Ala2155Val (c.6464C>T) is associated with Inborn genetic diseases (ClinVar).

How common is INTS1 p.Ala2155Val (c.6464C>T) in the general population?

INTS1 p.Ala2155Val (c.6464C>T) is ultra-rare (popmax 0.0284%, eas) (gnomAD).

What do computational predictors say about INTS1 p.Ala2155Val (c.6464C>T)?

AlphaMissense predicts likely benign (score 0.2807) — an in-silico prediction, not a clinical call.

INTS1 p.Ala2155Val

c.6464C>T · rs767857574 · VCV1439960

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

AlphaMissense

likely benign

0.2807 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0284%, eas)

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.2807	likely benign
REVEL	0.437	indeterminate
SaProt	LLR -4.44	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 0.57, phastCons 1
Regional constraint	o/e 1.09	unconstrained · MANE · 12 kb · p 0.001 · regional, not allelic
Overall
CADD	25.8	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 0.0284% East Asian · 12/42,278 alleles

Filtering AF 0.0164% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0128%

Overall 0.00386% 60/1,552,546 alleles · ultra-rare exomes 51/1,400,378 · genomes 9/152,168 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0284%	3,523
Admixed American	0.0115%	8,659
Remaining individualsnot grpmax-eligible	0.01%	9,974
Ashkenazi Jewishnot grpmax-eligible	0.00354%	28,216
European (non-Finnish)	0.00287%	34,808
African / African-American	0.00136%	73,284
South Asian	0.00118%	84,710

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.Ala2155Val
Coding: c.6464C>T
MANE Select: NM_001080453
dbSNP: rs767857574
Type: single nucleotide variant
Location: chr7:1470686 (GRCh38)
Gene constraint: LOEUF 0.785 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 75.49 · 8 PDB
Residue 2155: an α-helix; a UniProt-annotated variant site (in ndcagf; decreased protein abundance); a UniProt-annotated variant site (in ndcagf)

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 p.Ala2155Thr Uncertain significance ★ ⚠ same residue
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.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-ala2155val (accessed [today's date]).

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