NKAPD1

protein-coding

NKAP domain containing 1

Gene summary

Enables identical protein binding activity. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C11orf57

MANE transcript

NM_018195.4

Inheritance

—

ClinVar variants

U:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.24

Max pathogenic AF

—

Genomic locus

chr11:112,074,086-112,085,150

External References & Databases

Ensembl (ENSG00000150776)

Transcript & Mutation Effects

hg38 • Region Span ~11.1 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 NKAPD1 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018195.4. 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						0
missense			4 clinvar			4
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	5	0	0	5

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 27 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018195.4	RefSeq	NP_060665.3	5	MANE Select
ENST00000393047.8	Ensembl	ENSP00000376767.3	5	MANE Select
NM_001082969.2	RefSeq	NP_001076438.1	5	Standard
NM_001082970.2	RefSeq	NP_001076439.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

protein binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000393047
Coding exons: 5
Length: 11065
Individuals with no LoFs: 125729
Homozygous LoFs: 0
Heterozygous LoFs: 16
Defined: 125745
p: 0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.755	126	152	0.828	0.00000785	1956
Missense (PolyPhen)		38	58.143	0.65356		791
Synonymous	0.779	44	51.1	0.861	0.00000236	497
Loss of Function	2.51	3	12.6	0.238	5.27e-7	188

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000059	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00012	0.00012	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0967

Intolerance Scores

RVIS EVS: -0.21
RVIS percentile EVS: 38.58

Essentials

Essential (gene trap): H