TAMALIN

trafficking regulator and scaffold protein tamalin, the group of PDZ domain containing

Basic information

Region (hg38): 12:52006946-52015889

Previous symbols: [ "GRASP" ]

Links

ENSG00000161835 ∙ NCBI:160622 ∙ OMIM:612027 ∙ HGNC:18707 ∙ Uniprot:Q7Z6J2 ∙ 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 TAMALIN gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TAMALIN 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						0
missense			30	2	1	33
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	30	2	1

Variants in TAMALIN

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

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

Position	Type	Phenotype	Significance	ClinVar
12-52007026-C-T		not specified	Uncertain significance (Jan 22, 2024)
12-52007179-G-A		not specified	Uncertain significance (Jan 31, 2024)
12-52007195-T-C		not specified	Uncertain significance (Jun 18, 2021)
12-52007225-G-A		not specified	Uncertain significance (May 30, 2023)
12-52009202-C-T		not specified	Uncertain significance (Nov 15, 2023)
12-52009214-C-T			Benign (Jul 31, 2018)
12-52011114-C-T		not specified	Uncertain significance (Jul 21, 2022)
12-52011136-C-A		not specified	Uncertain significance (Jan 08, 2024)
12-52011138-C-G		not specified	Uncertain significance (Feb 27, 2024)
12-52013698-G-A		not specified	Uncertain significance (Nov 10, 2022)
12-52013702-G-T		not specified	Uncertain significance (Apr 08, 2024)
12-52013708-A-G		not specified	Uncertain significance (Oct 02, 2023)
12-52013732-G-A		not specified	Uncertain significance (Apr 22, 2024)
12-52013738-G-A		not specified	Uncertain significance (Feb 28, 2023)
12-52014189-C-T		not specified	Uncertain significance (Apr 27, 2023)
12-52014723-G-A		not specified	Uncertain significance (Sep 20, 2023)
12-52014907-C-T		not specified	Uncertain significance (Apr 19, 2023)
12-52014933-T-G		not specified	Uncertain significance (Jun 22, 2021)
12-52014934-T-A		not specified	Uncertain significance (Jun 22, 2021)
12-52014935-C-A		not specified	Likely benign (Jun 22, 2021)
12-52014939-C-G		not specified	Uncertain significance (Jun 22, 2021)
12-52014946-C-G		not specified	Uncertain significance (Jun 22, 2021)
12-52014975-C-T		not specified	Uncertain significance (Dec 19, 2022)
12-52014978-G-A		not specified	Uncertain significance (Nov 18, 2022)
12-52014990-G-A		not specified	Uncertain significance (Sep 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TAMALIN	protein_coding	protein_coding	ENST00000293662	8	8950

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.901	0.0987	125743	0	5	125748	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.49	117	172	0.679	0.0000112	2398
Missense in Polyphen		26	51.737	0.50254		588
Synonymous	0.741	66	74.1	0.890	0.00000461	867
Loss of Function	3.28	2	16.3	0.123	8.61e-7	191

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)	0.00000879	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in intracellular trafficking and contributes to the macromolecular organization of group 1 metabotropic glutamate receptors (mGluRs) at synapses. {ECO:0000250}.
• Pathway: phosphoinositides and their downstream targets (Consensus)

Recessive Scores

• pRec: 0.152

Haploinsufficiency Scores

• pHI: 0.647
• hipred: Y
• hipred_score: 0.697
• ghis: 0.432

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Grasp
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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); cellular phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan)

Gene ontology

• Biological process: signal transduction;protein localization;regulation of neurotransmitter receptor transport, endosome to postsynaptic membrane
• Cellular component: plasma membrane;postsynaptic density;cell junction;postsynaptic membrane;perinuclear region of cytoplasm;Schaffer collateral - CA1 synapse;glutamatergic synapse
• Molecular function: PDZ domain binding;ADP-ribosylation factor binding;identical protein binding