ANKRD42

protein-coding

ankyrin repeat domain 42, the group of Protein phosphatase 1 regulatory subunits|Ankyrin repeat domain containing

Gene summary

Predicted to enable NF-kappaB binding activity and cyclin-dependent protein serine/threonine kinase inhibitor activity. Predicted to act upstream of or within obsolete positive regulation of NF-kappaB transcription factor activity and positive regulation of cytokine production involved in inflammatory response. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001300975.2

Inheritance

—

ClinVar variants

U:74

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.82

Max pathogenic AF

—

Genomic locus

chr11:83,193,712-83,260,694

External References & Databases

Ensembl (ENSG00000137494)

Transcript & Mutation Effects

hg38 • Region Span ~67.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ANKRD42 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 70

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001300975.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar			2
missense			71 clinvar			71
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	74	0	0	74

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 37 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001300975.2	RefSeq	NP_001287904.1	11	MANE Select
ENST00000533342.6	Ensembl	ENSP00000435790.1	11	MANE Select
NM_001300972.2	RefSeq	NP_001287901.1	12	Standard
NM_001300973.2	RefSeq	NP_001287902.1	12	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000393392
Coding exons: 10
Length: 66956
Individuals with no LoFs: 125570
Homozygous LoFs: 0
Heterozygous LoFs: 177
Defined: 125747
p: 0.000704

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.134	205	210	0.974	0.0000101	2587
Missense (PolyPhen)		82	85.704	0.95678		1091
Synonymous	0.775	65	73.5	0.885	0.00000379	702
Loss of Function	0.762	17	20.7	0.819	0.00000106	250

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00043	0.00043	rare
Latino/Admixed American	0.00014	0.00014	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.0017	0.0017	notable
Finnish	0.0035	0.0035	notable
European (Non-Finnish)	0.00032	0.00032	rare
South Asian	0.00066	0.00065	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.104

Intolerance Scores

LoFtool: 0.849
RVIS EVS: 0.06
RVIS percentile EVS: 58.74

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.198

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium