MATCAP1

microtubule associated tyrosine carboxypeptidase 1

Basic information

Region (hg38): 16:67175599-67184040

Previous symbols: [ "KIAA0895L" ]

Links

ENSG00000196123 ∙ NCBI:653319 ∙ OMIM:619978 ∙ HGNC:34408 ∙ Uniprot:Q68EN5 ∙ 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 MATCAP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MATCAP1 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			39	1		40
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	39	1	0

Variants in MATCAP1

This is a list of pathogenic ClinVar variants found in the MATCAP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-67176891-G-A		not specified	Uncertain significance (Jan 16, 2024)
16-67176918-C-T		not specified	Uncertain significance (Jan 04, 2022)
16-67176944-G-A		not specified	Uncertain significance (Jul 17, 2023)
16-67176947-C-T		not specified	Uncertain significance (Apr 05, 2023)
16-67176948-G-A		not specified	Uncertain significance (Feb 13, 2024)
16-67178018-G-T		not specified	Uncertain significance (Dec 21, 2023)
16-67178238-C-T		not specified	Uncertain significance (Sep 09, 2024)
16-67178247-C-G		not specified	Uncertain significance (May 15, 2024)
16-67178276-C-T		not specified	Uncertain significance (May 09, 2022)
16-67178286-C-T		not specified	Uncertain significance (Jun 07, 2023)
16-67178307-A-G		not specified	Uncertain significance (Oct 20, 2023)
16-67178322-G-A		not specified	Uncertain significance (Dec 15, 2022)
16-67178465-G-A		not specified	Uncertain significance (Feb 22, 2023)
16-67178471-C-A		not specified	Uncertain significance (Nov 17, 2022)
16-67179441-C-T		not specified	Uncertain significance (Dec 02, 2022)
16-67179489-G-A		not specified	Uncertain significance (Apr 12, 2022)
16-67179502-G-A		not specified	Uncertain significance (Sep 20, 2023)
16-67179892-C-T		not specified	Uncertain significance (Dec 21, 2023)
16-67180078-T-G		not specified	Uncertain significance (Dec 04, 2024)
16-67180162-C-T		not specified	Uncertain significance (Nov 21, 2024)
16-67180163-G-A		not specified	Uncertain significance (Feb 27, 2024)
16-67180167-C-G		not specified	Uncertain significance (Mar 25, 2024)
16-67180204-C-A		not specified	Uncertain significance (Jan 23, 2024)
16-67180213-G-C		not specified	Uncertain significance (Jun 16, 2023)
16-67180214-C-T		not specified	Uncertain significance (Mar 19, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MATCAP1	protein_coding	protein_coding	ENST00000290881	6	8439

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00194	0.994	124774	0	21	124795	0.0000841

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.58	217	293	0.741	0.0000177	2982
Missense in Polyphen		51	97.189	0.52475		1131
Synonymous	1.41	97	116	0.834	0.00000605	991
Loss of Function	2.51	8	20.1	0.397	0.00000103	207

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000191	0.000188
Ashkenazi Jewish	0.00	0.00
East Asian	0.000336	0.000334
Finnish	0.00	0.00
European (Non-Finnish)	0.0000647	0.0000618
Middle Eastern	0.000336	0.000334
South Asian	0.000152	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.249
• rvis_EVS: 0.15
• rvis_percentile_EVS: 64.51

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.351
• ghis: 0.527

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.161

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: 4931428F04Rik