Is CENPI p.Ser361= (c.1083T>C) pathogenic?

CENPI p.Ser361= (c.1083T>C) is classified Likely benign in CENPI (ClinVar, Single submitter, 1 submitter; last evaluated 2022-07-01). Very rare (popmax 0.000786%, nfe).

How common is CENPI p.Ser361= (c.1083T>C) in the general population?

CENPI p.Ser361= (c.1083T>C) is very rare (popmax 0.000786%, nfe) (gnomAD).

CENPI p.Ser361=

c.1083T>C · rs893088033 · VCV2661052

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.000786%, nfe)

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 2.8	GERP -0.84, phastCons 1
Overall
CADD	10.06	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000786% European (non-Finnish) · 7/890,962 alleles

Filtering AF 0.000327% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00021%

Overall 0.000581% 7/1,203,916 alleles · very rare

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: CENPI
Protein: p.Ser361=
Coding: c.1083T>C
MANE Select: NM_001386188
dbSNP: rs893088033
Type: single nucleotide variant
Location: chrX:101128724 (GRCh38)
Structure: AlphaFold pLDDT 74.27 · 12 PDB

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

Similar variants

CENPI p.Val10Ile Benign ★★ same type
CENPI p.Val276Met Benign ★★ same type
CENPI c.1195+6A>G Uncertain significance ★ same type
CENPI c.687+8C>T Uncertain significance ★ same type
CENPI p.Ala147Gly Uncertain significance ★ ⚠ same type
CENPI p.Ala479Val Uncertain significance ★ same type
CENPI p.Ala674Asp Uncertain significance ★ ⚠ same type
CENPI p.Ala692Thr 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/cenpi-p-ser361 (accessed [today's date]).

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