CYTIP

Chr 2

cytohesin 1 interacting protein

Also known as: B3-1, CASP, CYBR, CYTHIP, HE, PSCDBP

NCBI Gene: 9595 ENSG00000115165 UniProt: O60759 OMIM: 604448

The protein encoded by this gene contains 2 leucine zipper domains and a putative C-terminal nuclear targeting signal, but does not have any hydrophobic regions. This protein is expressed weakly in resting NK and T cells. The encoded protein modulates the activation of ARF genes by CYTH1. This protein interacts with CYTH1 and SNX27 proteins and may act to sequester CYTH1 protein in the cytoplasm.[provided by RefSeq, Aug 2008]

OMIM Research

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.71

LOEUF

Multiple*

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

0.71LOEUF

pLI 0.002

Z-score 2.54

OE 0.39 (0.23–0.71)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

0.63Z-score

OE missense 0.88 (0.78–0.99)

180 obs / 205.5 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.39 (0.23–0.71)

0≤0.351.4

Missense OE?0.88 (0.78–0.99)

0≤0.61.4

Synonymous OE?0.94

0≤1.21.6

LoF obs/exp: 8 / 20.4Missense obs/exp: 180 / 205.5Syn Z: 0.42

Background carrier burden — how many people carry a rare variant somewhere in CYTIP?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 120

446 rare PASS variants

Rare truncating (LoF)

1 in 2,800

60 rare PASS variants

Rare synonymous (reference)

1 in 170

171 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for CYTIP. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 230	1 in 3,100
South Asian	~43k	1 in 68	1 in 1,600
Remaining (unassigned)	~30k	1 in 84	1 in 5,000
European (Finnish)	~27k	1 in 440	1 in 2,200
Admixed American	~22k	1 in 100	1 in 1,300
African / African American	~21k	1 in 150	1 in 2,100
East Asian	~20k	1 in 160	1 in 2,400
Ashkenazi Jewish	~13k	1 in 890	none seen
Middle Eastern	~2,884	1 in 110	≈ 1 in 2,900

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): 7 of 8 coding exons well covered in gnomAD exomes; exon 7 marginal. Genomes: 7 of 8 (exon 2 below).? see exons ↓