TAPT1

transmembrane anterior posterior transformation 1

Basic information

Region (hg38): 4:16160504-16227410

Links

ENSG00000169762 ∙ NCBI:202018 ∙ OMIM:612758 ∙ HGNC:26887 ∙ Uniprot:Q6NXT6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• complex lethal osteochondrodysplasia (Supportive), mode of inheritance: AR
• complex lethal osteochondrodysplasia (Strong), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TAPT1 gene.

• not provided (210 variants)
• Inborn genetic diseases (18 variants)
• Complex lethal osteochondrodysplasia (3 variants)
• Reduced bone mineral density;Abnormal long bone morphology;Short stature;Recurrent fractures;Scoliosis (1 variants)
• not specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TAPT1 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				32	5	37
missense			58	5	1	64
nonsense						0
start loss						0
frameshift						0
inframe indel			1			1
splice donor/acceptor (+/-2bp)		1				1
splice region			3	6	5	14
non coding			2	44	59	105
Total	0	1	61	81	65

Variants in TAPT1

This is a list of pathogenic ClinVar variants found in the TAPT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-16163339-C-T		Complex lethal osteochondrodysplasia	Uncertain significance (Apr 04, 2024)
4-16163398-C-T			Likely benign (Aug 31, 2021)
4-16163399-G-A		Inborn genetic diseases	Uncertain significance (Jun 29, 2023)
4-16163413-G-A		TAPT1-related disorder	Benign (Jan 30, 2024)
4-16163413-G-C			Uncertain significance (Apr 13, 2022)
4-16163413-G-T			Uncertain significance (Jun 20, 2022)
4-16163431-C-G			Uncertain significance (Sep 03, 2021)
4-16163431-C-T			Likely benign (Nov 30, 2021)
4-16163447-T-C		not specified	Benign/Likely benign (Dec 31, 2023)
4-16163469-T-C		Inborn genetic diseases	Uncertain significance (Sep 09, 2021)
4-16163481-T-C		Inborn genetic diseases	Uncertain significance (Nov 10, 2022)
4-16163490-T-C			Uncertain significance (Jun 11, 2022)
4-16163500-G-C			Likely benign (Aug 22, 2022)
4-16163505-T-C		Inborn genetic diseases	Likely benign (Dec 09, 2023)
4-16163513-G-A		Inborn genetic diseases	Uncertain significance (Aug 22, 2022)
4-16163515-C-T			Likely benign (Jul 08, 2023)
4-16163565-G-A			Likely benign (Mar 29, 2019)
4-16166331-C-T			Benign (Aug 25, 2018)
4-16166338-C-T			Benign (Apr 03, 2019)
4-16166620-G-T			Likely benign (Jul 18, 2023)
4-16166621-G-C			Benign (Dec 22, 2023)
4-16166623-C-T			Benign/Likely benign (Jan 30, 2024)
4-16166633-C-T			Uncertain significance (Apr 09, 2022)
4-16166639-A-C			Uncertain significance (Apr 20, 2022)
4-16166640-G-A			Likely benign (Jun 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TAPT1	protein_coding	protein_coding	ENST00000405303	14	66906

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0321	0.968	124627	0	8	124635	0.0000321

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.92	157	241	0.652	0.0000117	3679
Missense in Polyphen		49	111.07	0.44116		1560
Synonymous	0.586	77	83.8	0.919	0.00000417	1059
Loss of Function	3.13	7	23.3	0.300	0.00000111	365

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000904	0.0000904
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000284	0.0000265
Middle Eastern	0.00	0.00
South Asian	0.0000659	0.0000654
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in primary cilia formation (PubMed:26365339). May act as a downstream effector of HOXC8 possibly by transducing or transmitting extracellular information required for axial skeletal patterning during development (By similarity). May be involved in cartilage and bone development (By similarity). May play a role in the differentiation of cranial neural crest cells (By similarity). {ECO:0000250|UniProtKB:A2BIE7, ECO:0000250|UniProtKB:Q4VBD2, ECO:0000269|PubMed:26365339}.
• Disease: DISEASE: Osteochondrodysplasia, complex lethal, Symoens-Barnes- Gistelinck type (OCLSBG) [MIM:616897]: An autosomal recessive, lethal syndrome characterized by severe hypomineralization of the entire skeleton, severe osteopenia, microcephaly, multiple intra- uterine fractures, and multiple congenital developmental anomalies affecting the brain, lungs, and kidneys. {ECO:0000269|PubMed:26365339}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Recessive Scores

• pRec: 0.102

Intolerance Scores

• rvis_EVS: 0.31
• rvis_percentile_EVS: 72.38

Haploinsufficiency Scores

• pHI: 0.271
• hipred: Y
• hipred_score: 0.591
• ghis: 0.466

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.368

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tapt1
• Phenotype: digestive/alimentary phenotype; skeleton phenotype; growth/size/body region phenotype; hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); craniofacial phenotype

Zebrafish Information Network

• Gene name: tapt1b
• Affected structure: cranial neural crest cell
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: ossification;in utero embryonic development;G protein-coupled receptor signaling pathway;post-embryonic development;neural crest cell development;cell projection organization;maintenance of protein localization in endoplasmic reticulum;positive regulation of cilium assembly;embryonic skeletal system development;cartilage development;positive regulation of cartilage development;positive regulation of bone development
• Cellular component: endoplasmic reticulum;centrosome;integral component of membrane;integral component of endoplasmic reticulum membrane;ciliary basal body
• Molecular function: growth hormone-releasing hormone receptor activity