Is CEP170B p.Phe490= (c.1470C>T) pathogenic?

CEP170B p.Phe490= (c.1470C>T) is classified Likely benign in CEP170B (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-07-16). Ultra-rare (popmax 0.0602%, afr); Associated with CEP170B-related disorder.

What condition is associated with CEP170B p.Phe490= (c.1470C>T)?

CEP170B p.Phe490= (c.1470C>T) is associated with CEP170B-related disorder (ClinVar).

How common is CEP170B p.Phe490= (c.1470C>T) in the general population?

CEP170B p.Phe490= (c.1470C>T) is ultra-rare (popmax 0.0602%, afr) (gnomAD).

CEP170B p.Phe490=

c.1470C>T · rs370195295 · VCV3050366

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0602%, afr)

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 -9.4	GERP -2.8
Overall
CADD	3.584	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0602% African / African-American · 44/73,138 alleles

Filtering AF 0.0461% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.041%

Overall 0.00958% 148/1,544,616 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0602%	1,662
South Asian	0.00954%	10,480
European (non-Finnish)	0.00759%	13,182
Remaining individualsnot grpmax-eligible	0.00667%	14,986
Admixed American	0.00391%	25,597
Finnishnot grpmax-eligible	0.00373%	26,797
East Asian	0.00244%	40,956

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.Phe490=
Coding: c.1470C>T
MANE Select: NM_001112726
dbSNP: rs370195295
Type: single nucleotide variant
Location: chr14:104884249 (GRCh38)
Gene constraint: LOEUF 0.682 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 47.31
Residue 490: 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 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
CEP170B p.Ala302Val Likely benign same condition
CEP170B p.Ala369Val 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-phe490 (accessed [today's date]).

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