Is CEP19 p.His58= (c.174C>T) pathogenic?

CEP19 p.His58= (c.174C>T) is classified Likely benign in CEP19 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-01-29). Absent from gnomAD v4.1.

How common is CEP19 p.His58= (c.174C>T) in the general population?

CEP19 p.His58= (c.174C>T) is absent from gnomAD v4.1 (gnomAD).

CEP19 p.His58=

c.174C>T · rs2108662922 · VCV1153859

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 5.2	GERP 1.4, phastCons 1
Overall
CADD	7.494	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: CEP19
Protein: p.His58=
Coding: c.174C>T
MANE Select: NM_032898
dbSNP: rs2108662922
Type: single nucleotide variant
Location: chr3:196707869 (GRCh38)
Gene constraint: LOEUF 1.208 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 82.85

Full CEP19 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CEP19 p.His58Tyr Uncertain significance ★ same residue
CEP19 p.His58fs Uncertain significance ★ same residue
CEP19 p.Arg32His Uncertain significance ★★ same type
CEP19 p.Arg37Ter Uncertain significance ★★ same type
CEP19 p.Arg95Trp Uncertain significance ★★ same type
CEP19 p.Asn54Ser Uncertain significance ★★ same type
CEP19 p.Gly27Arg Uncertain significance ★★ same type
CEP19 p.Ile33Val 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/cep19-p-his58 (accessed [today's date]).

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