Is CANT1 p.Ala82Val (c.245C>T) pathogenic?

CANT1 p.Ala82Val (c.245C>T) is classified Conflicting classifications of pathogenicity in CANT1 (ClinVar, Conflicting submitters, 2 submitters; last evaluated 2024-10-08). AlphaMissense: likely benign (0.0647); Ultra-rare (popmax 0.0264%, sas); Associated with Inborn genetic diseases.

What condition is associated with CANT1 p.Ala82Val (c.245C>T)?

CANT1 p.Ala82Val (c.245C>T) is associated with Inborn genetic diseases (ClinVar).

How common is CANT1 p.Ala82Val (c.245C>T) in the general population?

CANT1 p.Ala82Val (c.245C>T) is ultra-rare (popmax 0.0264%, sas) (gnomAD).

What do computational predictors say about CANT1 p.Ala82Val (c.245C>T)?

AlphaMissense predicts likely benign (score 0.0647) — an in-silico prediction, not a clinical call.

CANT1 p.Ala82Val

c.245C>T · rs142062082 · VCV2327971

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.0647 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0264%, sas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.0647	likely benign
REVEL	0.167	moderately benign-leaning
SaProt	LLR -6.61	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -1.4	GERP -3
Regional constraint	o/e 0.93	unconstrained · MANE · 594 bp · p 0.23 · regional, not allelic
Overall
CADD	0.2	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 0.0264% South Asian · 24/91,078 alleles

Filtering AF 0.0181% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0154%

Overall 0.00508% 82/1,613,522 alleles · ultra-rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0264%	3,795
African / African-American	0.0174%	5,759
Admixed American	0.0167%	5,998
Middle Eastern	0.0164%	6,080
Remaining individualsnot grpmax-eligible	0.0064%	15,613
European (non-Finnish)	0.00254%	39,327

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: CANT1
Protein: p.Ala82Val
Coding: c.245C>T
MANE Select: NM_001159773
dbSNP: rs142062082
Type: single nucleotide variant
Location: chr17:78997378 (GRCh38)
Gene constraint: LOEUF 1.239 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 89.47 · 4 PDB

Full CANT1 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

CANT1 p.Ala82= Conflicting classifications of pathogenicity ★ same residue
CANT1 p.Arg300Cys Pathogenic/Likely pathogenic ★★ same condition
CANT1 p.Arg183Gln Uncertain significance ★★ ⚠ same condition
CANT1 p.Arg183Trp Uncertain significance ★★ ⚠ same condition
CANT1 p.Arg270Gln Uncertain significance ★★ ⚠ same condition
CANT1 p.Arg38His Uncertain significance ★★ ⚠ same condition
CANT1 p.Arg63His Uncertain significance ★★ ⚠ same condition
CANT1 p.Arg63Ser 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/cant1-p-ala82val (accessed [today's date]).

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