Is CEP170B p.Tyr91= (c.273C>T) pathogenic?

CEP170B p.Tyr91= (c.273C>T) is classified Likely benign in CEP170B (ClinVar, Single submitter, 1 submitter; last evaluated 2022-07-01). Very rare (popmax 0.00403%, afr).

How common is CEP170B p.Tyr91= (c.273C>T) in the general population?

CEP170B p.Tyr91= (c.273C>T) is very rare (popmax 0.00403%, afr) (gnomAD).

CEP170B p.Tyr91=

c.273C>T · rs747223873 · VCV2644624

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00403%, afr)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · C>A here scores Δ0.32 · evaluated, not missing
Constraint at this position
Conservation	phyloP -10	GERP -3.6
Overall
CADD	1.491	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00403% African / African-American · 3/74,534 alleles

Filtering AF 0.0013% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00109%

Overall 0.00174% 28/1,605,562 alleles · very rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00403%	24,845
Remaining individualsnot grpmax-eligible	0.00321%	31,117
European (non-Finnish)	0.00195%	51,163

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.Tyr91=
Coding: c.273C>T
MANE Select: NM_001112726
dbSNP: rs747223873
Type: single nucleotide variant
Location: chr14:104877962 (GRCh38)
Gene constraint: LOEUF 0.682 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 47.31

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

Similar variants

CEP170B p.Lys368Glu Uncertain significance ★★ same type
CEP170B p.Pro148Leu Uncertain significance ★★ same type
CEP170B p.Ala259Val Benign ★★ same type
CEP170B p.Arg147= Benign ★★ same type
CEP170B p.Ala1053Val Uncertain significance ★ same type
CEP170B p.Ala1062Val Uncertain significance ★ same type
CEP170B p.Ala1083Val Uncertain significance ★ same type
CEP170B p.Ala1091Thr 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/cep170b-p-tyr91 (accessed [today's date]).

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