TCP11L2

protein-coding

t-complex 11 like 2

Gene summary

Predicted to be involved in muscle cell migration and signal transduction. Located in nuclear speck. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_152772.3

Inheritance

—

ClinVar variants

U:77B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.87

Max pathogenic AF

—

Genomic locus

chr12:106,301,929-106,347,538

External References & Databases

Ensembl (ENSG00000166046)

Transcript & Mutation Effects

hg38 • Region Span ~45.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

schizophreniaNO_KNOWN

Inheritance Pattern: Unknown

Disease ID:MONDO:0005090

Submitter: Labcorp Genetics (formerly Invitae)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TCP11L2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 70

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_152772.3. 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	2 clinvar		3
missense			71 clinvar	2 clinvar		73
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	0	77	4	0	81

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 44 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_152772.3	RefSeq	NP_689985.1	9	MANE Select
ENST00000299045.8	Ensembl	ENSP00000299045.3	9	MANE Select
NM_001286262.2	RefSeq	NP_001273191.1	6	Standard
ENST00000546625.5	Ensembl	ENSP00000449123.1	5	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000299045
Coding exons: 9
Length: 45087
Individuals with no LoFs: 125619
Homozygous LoFs: 0
Heterozygous LoFs: 129
Defined: 125748
p: 0.000513

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.130	282	276	1.02	0.0000137	3429
Missense (PolyPhen)		92	93.243	0.98667		1186
Synonymous	1.20	86	101	0.849	0.00000521	993
Loss of Function	0.589	20	23.1	0.868	0.00000122	276

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00050	0.00049	rare
Latino/Admixed American	0.000087	0.000087	rare
Ashkenazi Jewish	0.0053	0.0049	notable
East Asian	0.00054	0.00054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00037	0.00037	rare
South Asian	0.00043	0.00042	rare
Other	0.00066	0.00065	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.954
RVIS EVS: 0.04
RVIS percentile EVS: 57.41

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.254

Gene Damage Prediction

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