Is CEP170B p.Ser868= (c.2604C>T) pathogenic?

CEP170B p.Ser868= (c.2604C>T) is classified Likely benign in CEP170B (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-05-23). Rare (popmax 0.811%, eas); Associated with CEP170B-related disorder.

What condition is associated with CEP170B p.Ser868= (c.2604C>T)?

CEP170B p.Ser868= (c.2604C>T) is associated with CEP170B-related disorder (ClinVar).

How common is CEP170B p.Ser868= (c.2604C>T) in the general population?

CEP170B p.Ser868= (c.2604C>T) is rare (popmax 0.811%, eas) (gnomAD).

CEP170B p.Ser868=

c.2604C>T · rs200838340 · VCV3038428

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.811%, eas)

Conditions

CEP170B-related disorder

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 0.54	GERP -0.86, phastCons 1
Overall
CADD	9.055	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.811% East Asian · 364/44,876 alleles

Filtering AF 0.742% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.715%

Overall 0.0271% 436/1,611,022 alleles · rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.811%	123
South Asian	0.0494%	2,024
Remaining individualsnot grpmax-eligible	0.0368%	2,715
Admixed American	0.00333%	30,013
European (non-Finnish)	0.00017%	589,911

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: CEP170B
Protein: p.Ser868=
Coding: c.2604C>T
MANE Select: NM_001112726
dbSNP: rs200838340
Type: single nucleotide variant
Location: chr14:104886843 (GRCh38)
Gene constraint: LOEUF 0.682 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 47.31
Residue 868: the 'disordered' region

Full CEP170B gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

CEP170B-related disorder

Similar variants

CEP170B p.Ser868Asn Uncertain significance ★ same residue
CEP170B p.Ser868Cys Uncertain significance ★ same residue
CEP170B c.3879-7G>C Benign same condition
CEP170B c.3879-8G>A Benign same condition
CEP170B c.4271+8G>A Likely benign same condition
CEP170B c.4365+7G>A Likely benign same condition
CEP170B p.Ala1177= Likely benign same condition
CEP170B p.Ala127= Likely benign 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/cep170b-p-ser868 (accessed [today's date]).

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