CDIN1

Chr 15AR

CDAN1 interacting nuclease 1

Also known as: C15orf41, HH114

NCBI Gene: 84529 ENSG00000186073 UniProt: Q9Y2V0 OMIM: 615626

This gene encodes a protein with two predicted helix-turn-helix domains. Mutations in this gene were found in families with congenital dyserythropoietic anemia type Ib. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Mar 2014]

GeneReviews OMIM Research

GeneReviews OMIM ResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

Dyserythropoietic anemia, congenital, type IbMIM #615631

Clinical highlights

Gene–disease validity

Not independently assessedOMIM lists Dyserythropoietic anemia, congenital, type Ib; no ClinGen or GenCC tier

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.05

LOEUF

Mechanism· predicted

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GeneReview available — CDIN1

Authoritative clinical overview · Recommended first read

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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.05LOEUF

pLI 0.000

Z-score 1.38

OE 0.66 (0.43–1.05)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.47Z-score

OE missense 0.89 (0.77–1.03)

129 obs / 145.0 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.66 (0.43–1.05)

0≤0.351.4

Missense OE?0.89 (0.77–1.03)

0≤0.61.4

Synonymous OE?0.81

0≤1.21.6

LoF obs/exp: 13 / 19.6Missense obs/exp: 129 / 145.0Syn Z: 1.15

Background carrier burden — how many people carry a rare variant somewhere in CDIN1?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 140

364 rare PASS variants

Rare truncating (LoF)

1 in 2,300

83 rare PASS variants

Rare synonymous (reference)

1 in 510

131 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for CDIN1. 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 150	1 in 2,100
South Asian	~43k	1 in 230	1 in 3,500
Remaining (unassigned)	~30k	1 in 130	1 in 3,300
European (Finnish)	~27k	1 in 240	≈ 1 in 13,000
Admixed American	~22k	1 in 110	1 in 2,100
African / African American	~21k	1 in 110	1 in 3,600
East Asian	~20k	1 in 190	1 in 2,100
Ashkenazi Jewish	~13k	≈ 1 in 4,300	none seen
Middle Eastern	~2,884	1 in 160	none seen

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): All 11 coding exons well covered in gnomAD exomes and genomes.? see exons ↓