Is CANT1 p.Ala360Asp (c.1079C>A) pathogenic?

CANT1 p.Ala360Asp (c.1079C>A) is classified Pathogenic in CANT1 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2011-01-01). AlphaMissense: likely pathogenic (0.9869); Absent from gnomAD v4.1; Associated with Desbuquois dysplasia 1.

What condition is associated with CANT1 p.Ala360Asp (c.1079C>A)?

CANT1 p.Ala360Asp (c.1079C>A) is associated with Desbuquois dysplasia 1 (ClinVar).

How common is CANT1 p.Ala360Asp (c.1079C>A) in the general population?

CANT1 p.Ala360Asp (c.1079C>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CANT1 p.Ala360Asp (c.1079C>A)?

AlphaMissense predicts likely pathogenic (score 0.9869) — an in-silico prediction, not a clinical call.

CANT1 p.Ala360Asp

c.1079C>A · rs387907081 · VCV31019

Pathogenic No assertion criteria

Classification

Pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9869 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Desbuquois dysplasia 1

Computational evidence

Protein change
AlphaMissense	0.9869	likely pathogenic ✓ concordant with ClinVar · top 4% in CANT1
REVEL	0.944	strongly pathogenic-leaning
SaProt	LLR -16.27	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 9.7	GERP 1.6, phastCons 1
Regional constraint	o/e 1.04	unconstrained · MANE · 1,531 bp · p 0.53 · regional, not allelic
Overall
CADD	31.0	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

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: CANT1
Protein: p.Ala360Asp
Coding: c.1079C>A
MANE Select: NM_001159773
dbSNP: rs387907081
Type: single nucleotide variant
Location: chr17:78993677 (GRCh38)
Gene constraint: LOEUF 1.239 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 89.47 · 4 PDB
Residue 360: a UniProt-annotated variant site (in dbqd1; affects protein secretion); a β-strand

Full CANT1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Desbuquois dysplasia 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CANT1 c.836-9G>A Pathogenic/Likely pathogenic ★★ same condition
CANT1 p.Arg300Cys Pathogenic/Likely pathogenic ★★ same condition
CANT1 p.Glu215Lys Pathogenic/Likely pathogenic ★★ same condition
CANT1 p.Pro245Leu Pathogenic/Likely pathogenic ★★ same condition
CANT1 p.Pro299Leu Likely pathogenic ★★ same condition
CANT1 p.Trp247Arg Likely pathogenic ★★ same condition
CANT1 p.Val226Met Pathogenic ★★ same condition
CANT1 c.835+6A>G 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-ala360asp (accessed [today's date]).

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