KAZALD1

Kazal type serine peptidase inhibitor domain 1, the group of I-set domain containing

Basic information

Region (hg38): 10:101061988-101068131

Links

ENSG00000107821 ∙ NCBI:81621 ∙ OMIM:609208 ∙ HGNC:25460 ∙ Uniprot:Q96I82 ∙ 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 KAZALD1 gene.

• Inborn genetic diseases (20 variants)
• not provided (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KAZALD1 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					2	2
missense			21		2	23
nonsense				1		1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	1	4

Variants in KAZALD1

This is a list of pathogenic ClinVar variants found in the KAZALD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-101062675-C-T		not specified	Uncertain significance (Dec 02, 2021)
10-101062679-C-T			Benign (Jul 16, 2018)
10-101062739-G-C		not specified	Uncertain significance (May 27, 2022)
10-101062786-G-C		not specified	Uncertain significance (Nov 01, 2022)
10-101062803-A-T			Benign (Feb 25, 2018)
10-101062891-G-T		not specified	Uncertain significance (Sep 12, 2023)
10-101062908-C-T		not specified	Uncertain significance (Jan 31, 2022)
10-101062912-A-C		not specified	Uncertain significance (Aug 10, 2021)
10-101062914-T-C		not specified	Uncertain significance (Oct 12, 2022)
10-101062930-G-T		not specified	Uncertain significance (Aug 08, 2023)
10-101062944-C-T		not specified	Uncertain significance (Jan 27, 2022)
10-101062980-T-A		not specified	Uncertain significance (Oct 12, 2021)
10-101063031-C-T		not specified	Uncertain significance (Apr 04, 2023)
10-101063071-T-G		not specified	Uncertain significance (May 05, 2023)
10-101064299-G-A		not specified	Uncertain significance (Mar 29, 2022)
10-101064326-T-C		not specified	Uncertain significance (Jan 23, 2023)
10-101064345-C-T		not specified	Uncertain significance (Feb 06, 2023)
10-101064348-T-C		not specified	Uncertain significance (Apr 04, 2023)
10-101064359-G-C		not specified	Uncertain significance (Mar 24, 2023)
10-101064403-C-A		not specified	Uncertain significance (Dec 21, 2022)
10-101064420-A-G			Uncertain significance (Aug 15, 2021)
10-101064548-C-T			Benign (Jul 16, 2018)
10-101064559-G-A		not specified	Uncertain significance (Jan 31, 2023)
10-101064595-G-A			Benign (Feb 25, 2018)
10-101064622-C-T		not specified	Uncertain significance (Aug 16, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KAZALD1	protein_coding	protein_coding	ENST00000370200	4	6291

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.67e-7	0.336	125676	0	63	125739	0.000251

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.122	164	168	0.973	0.00000824	1900
Missense in Polyphen		80	69.046	1.1586		782
Synonymous	0.326	70	73.6	0.952	0.00000365	656
Loss of Function	0.418	10	11.5	0.867	4.97e-7	115

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000873	0.0000873
Ashkenazi Jewish	0.00239	0.00238
East Asian	0.000110	0.000109
Finnish	0.000294	0.000139
European (Non-Finnish)	0.000247	0.000220
Middle Eastern	0.000110	0.000109
South Asian	0.000131	0.000131
Other	0.000383	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the proliferation of osteoblasts during bone formation and bone regeneration. Promotes matrix assembly (By similarity). {ECO:0000250}.

Intolerance Scores

• loftool: 0.561
• rvis_EVS: 0.9
• rvis_percentile_EVS: 89.39

Haploinsufficiency Scores

• pHI: 0.119
• hipred: N
• hipred_score: 0.261
• ghis: 0.392

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0401

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Kazald1

Gene ontology

• Biological process: ossification;regulation of cell growth;multicellular organism development;cell differentiation;extracellular matrix organization
• Cellular component: interstitial matrix
• Molecular function: insulin-like growth factor binding