NCKIPSD

NCK interacting protein with SH3 domain

Basic information

Region (hg38): 3:48673844-48686364

Links

ENSG00000213672 ∙ NCBI:51517 ∙ OMIM:606671 ∙ HGNC:15486 ∙ Uniprot:Q9NZQ3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NCKIPSD gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NCKIPSD gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			61	4		65
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2		2
non coding						0
Total	0	0	61	4	1

Variants in NCKIPSD

This is a list of pathogenic ClinVar variants found in the NCKIPSD region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
3-48674603-G-A		not specified	Uncertain significance (Dec 21, 2022)
3-48674614-C-T		not specified	Uncertain significance (Oct 12, 2021)
3-48674617-T-C		not specified	Uncertain significance (Feb 06, 2024)
3-48674671-G-C		not specified	Uncertain significance (Jun 28, 2022)
3-48674678-G-A		not specified	Uncertain significance (Dec 14, 2023)
3-48674684-G-A		not specified	Uncertain significance (Oct 22, 2024)
3-48674712-T-C		not specified	Uncertain significance (Jan 23, 2024)
3-48674714-T-C		not specified	Likely benign (Dec 05, 2022)
3-48674720-G-A		not specified	Uncertain significance (Aug 10, 2024)
3-48674744-G-A		not specified	Uncertain significance (Feb 12, 2025)
3-48678587-C-T		not specified	Uncertain significance (Jan 08, 2024)
3-48678596-G-A		not specified	Uncertain significance (May 11, 2022)
3-48678632-G-A		not specified	Uncertain significance (Jan 29, 2025)
3-48678658-C-T		not specified	Uncertain significance (Sep 15, 2021)
3-48678667-A-G		not specified	Uncertain significance (Apr 08, 2024)
3-48678694-T-G		not specified	Uncertain significance (Mar 13, 2023)
3-48678697-G-C		not specified	Uncertain significance (Oct 11, 2024)
3-48678724-C-A		not specified	Uncertain significance (Jun 30, 2022)
3-48678928-C-T		not specified	Likely benign (Apr 26, 2023)
3-48678957-T-C		not specified	Uncertain significance (Nov 10, 2022)
3-48679070-T-G		not specified	Uncertain significance (Nov 07, 2022)
3-48679181-G-A		not specified	Uncertain significance (Jul 02, 2024)
3-48679580-G-A		not specified	Uncertain significance (Dec 05, 2022)
3-48679634-G-A		not specified	Uncertain significance (Nov 07, 2024)
3-48679684-G-A			Benign (Jun 21, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NCKIPSD	protein_coding	protein_coding	ENST00000294129	13	22434

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000223	1.00	125643	0	105	125748	0.000418

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.607	400	436	0.918	0.0000266	4590
Missense in Polyphen		133	143.32	0.92802		1532
Synonymous	0.833	169	183	0.922	0.0000111	1564
Loss of Function	3.27	12	32.0	0.375	0.00000178	342

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000481	0.000479
Ashkenazi Jewish	0.00	0.00
East Asian	0.00386	0.00381
Finnish	0.00	0.00
European (Non-Finnish)	0.000143	0.000141
Middle Eastern	0.00386	0.00381
South Asian	0.000230	0.000229
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Has an important role in stress fiber formation induced by active diaphanous protein homolog 1 (DRF1). Induces microspike formation, in vivo (By similarity). In vitro, stimulates N-WASP- induced ARP2/3 complex activation in the absence of CDC42 (By similarity). May play an important role in the maintenance of sarcomeres and/or in the assembly of myofibrils into sarcomeres. Implicated in regulation of actin polymerization and cell adhesion. Plays a role in angiogenesis. {ECO:0000250, ECO:0000269|PubMed:22419821}.
• Pathway: Signal Transduction;Fcgamma receptor (FCGR) dependent phagocytosis;Innate Immune System;Immune System;RHO GTPases Activate WASPs and WAVEs;RHO GTPase Effectors;Signaling by Rho GTPases;Regulation of actin dynamics for phagocytic cup formation (Consensus)

Recessive Scores

• pRec: 0.109

Intolerance Scores

• loftool: 0.845
• rvis_EVS: -1
• rvis_percentile_EVS: 8.54

Haploinsufficiency Scores

• pHI: 0.0908
• hipred: Y
• hipred_score: 0.756
• ghis: 0.641

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.879

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nckipsd
• Phenotype: cellular phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: NLS-bearing protein import into nucleus;cytoskeleton organization;signal transduction;positive regulation of neuron projection development;Fc-gamma receptor signaling pathway involved in phagocytosis
• Cellular component: cytosol;intermediate filament;COP9 signalosome
• Molecular function: protein binding;cytoskeletal protein binding;SH3 domain binding