MINDY2

Chr 15

MINDY lysine 48 deubiquitinase 2

Also known as: FAM63B

NCBI Gene: 54629 ENSG00000128923 UniProt: Q8NBR6 OMIM: 618408

Enables peptidase activity and polyubiquitin modification-dependent protein binding activity. Predicted to be involved in chromatin remodeling and proteolysis. Located in nucleoplasm. [provided by Alliance of Genome Resources, Jul 2025]

OMIM Research

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.70

LOEUF

GOF

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

0.70LOEUF

pLI 0.000

Z-score 2.83

OE 0.44 (0.28–0.70)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

-0.56Z-score

OE missense 1.09 (1.00–1.19)

361 obs / 332.3 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?0.44 (0.28–0.70)

0≤0.351.4

Missense OE?1.09 (1.00–1.19)

0≤0.61.4

Synonymous OE?1.26

0≤1.21.6

LoF obs/exp: 13 / 29.6Missense obs/exp: 361 / 332.3Syn Z: -2.34

Background carrier burden — how many people carry a rare variant somewhere in MINDY2?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 68

928 rare PASS variants

Rare truncating (LoF)

1 in 2,500

121 rare PASS variants

Rare synonymous (reference)

1 in 160

398 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for MINDY2. 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 74	1 in 2,800
South Asian	~43k	1 in 63	1 in 2,600
Remaining (unassigned)	~30k	1 in 62	1 in 3,000
European (Finnish)	~27k	1 in 280	1 in 4,400
Admixed American	~22k	1 in 55	1 in 1,300
African / African American	~21k	1 in 74	1 in 2,000
East Asian	~20k	1 in 96	1 in 1,400
Ashkenazi Jewish	~13k	1 in 240	≈ 1 in 13,000
Middle Eastern	~2,884	1 in 68	≈ 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): 6 of 9 coding exons well covered in gnomAD exomes; exons 2, 3, 5 marginal. Genomes: all 9.? see exons ↓