MATCAP1

protein-coding

microtubule associated tyrosine carboxypeptidase 1

Gene summary

Enables tubulin-tyrosine carboxypeptidase activity. Predicted to be involved in brain development. Is active in microtubule. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

KIAA0895L

MANE transcript

NM_001040715.2

Inheritance

—

ClinVar variants

U:76B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.4

Max pathogenic AF

—

Genomic locus

chr16:67,175,599-67,184,040

External References & Databases

Ensembl (ENSG00000196123)

Transcript & Mutation Effects

hg38 • Region Span ~8.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to MATCAP1 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 75

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001040715.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar			1
missense			74 clinvar	1 clinvar		75
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	76	1	0	77

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 25 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001040715.2	RefSeq	NP_001035805.1	6	MANE Select
ENST00000563902.2	Ensembl	ENSP00000456838.1	6	MANE Select
NM_001369680.1	RefSeq	NP_001356609.1	6	Standard
NM_001369681.1	RefSeq	NP_001356610.1	6	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000290881
Coding exons: 6
Length: 8439
Individuals with no LoFs: 124774
Homozygous LoFs: 0
Heterozygous LoFs: 21
Defined: 124795
p: 0.0000841

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.58	217	293	0.741	0.0000177	2982
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00013	0.00013	rare
Latino/Admixed American	0.000059	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00034	0.00033	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000065	0.000062	rare
South Asian	0.00015	0.00013	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.249
RVIS EVS: 0.15
RVIS percentile EVS: 64.51

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.161

Gene Damage Prediction

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