Is CYLC1 p.Ser273= (c.819A>T) pathogenic?

CYLC1 p.Ser273= (c.819A>T) is classified Likely benign in CYLC1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-12-01). Absent from gnomAD v4.1.

How common is CYLC1 p.Ser273= (c.819A>T) in the general population?

CYLC1 p.Ser273= (c.819A>T) is absent from gnomAD v4.1 (gnomAD).

CYLC1 p.Ser273=

c.819A>T · rs1022918879 · VCV3025797

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

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 1.4	GERP 0.58, phastCons 0.68
Overall
CADD	5.666	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: CYLC1
Protein: p.Ser273=
Coding: c.819A>T
MANE Select: NM_021118
dbSNP: rs1022918879
Type: single nucleotide variant
Location: chrX:83873527 (GRCh38)
Structure: AlphaFold pLDDT 45.68
Residue 273: the 'disordered' region

Full CYLC1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CYLC1 p.Ala554Ser Uncertain significance ★ ⚠ same type
CYLC1 p.Ala595Val Uncertain significance ★ ⚠ same type
CYLC1 p.Ala611Asp Uncertain significance ★ ⚠ same type
CYLC1 p.Arg344Met Uncertain significance ★ ⚠ same type
CYLC1 p.Arg623His Uncertain significance ★ ⚠ same type
CYLC1 p.Arg637Ser Uncertain significance ★ ⚠ same type
CYLC1 p.Asn156Asp Uncertain significance ★ ⚠ same type
CYLC1 p.Asn194Ser Uncertain significance ★ ⚠ 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/cylc1-p-ser273 (accessed [today's date]).

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