Is ATL1 p.Cys260= (c.780T>C) pathogenic?

ATL1 p.Cys260= (c.780T>C) is classified Likely benign in ATL1 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2019-07-11). Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with ATL1 p.Cys260= (c.780T>C)?

ATL1 p.Cys260= (c.780T>C) is associated with Inborn genetic diseases (ClinVar).

How common is ATL1 p.Cys260= (c.780T>C) in the general population?

ATL1 p.Cys260= (c.780T>C) is absent from gnomAD v4.1 (gnomAD).

ATL1 p.Cys260=

c.780T>C · rs1555365177 · VCV512998

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.18	GERP -3.7, phastCons 0.99
Overall
CADD	8.672	PHRED · no single calibrated threshold — expert panels disagree

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: ATL1
Protein: p.Cys260=
Coding: c.780T>C
MANE Select: NM_015915
dbSNP: rs1555365177
Type: single nucleotide variant
Location: chr14:50614429 (GRCh38)
Gene constraint: LOEUF 0.57 · pLI 0.36 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 86.49 · 14 PDB
Residue 260: an α-helix; the gb1/rhd3-type g domain

Full ATL1 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

ATL1 p.Lys407Met Pathogenic/Likely pathogenic ★★ same condition
ATL1 c.630+3G>A Uncertain significance ★★ same condition
ATL1 p.Ala200Thr Uncertain significance ★★ ⚠ same condition
ATL1 p.Ala229Gly Uncertain significance ★★ ⚠ same condition
ATL1 p.Arg323Gln Uncertain significance ★★ ⚠ same condition
ATL1 p.Asn263Ser Uncertain significance ★★ ⚠ same condition
ATL1 p.Asn318Ile Uncertain significance ★★ ⚠ same condition
ATL1 p.Asp230Asn 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/atl1-p-cys260 (accessed [today's date]).

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