TMCC2

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					2 clinvar	2
missense			81 clinvar	2 clinvar	1 clinvar	84
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	82	2	3	87

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 29 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_014858.4	RefSeq	NP_055673.2	5	MANE Select
ENST00000358024.8	Ensembl	ENSP00000350718.3	5	MANE Select
NM_001242925.2	RefSeq	NP_001229854.1	4	Standard
NM_001297611.2	RefSeq	NP_001284540.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

amyloid precursor protein metabolic process

Molecular Function

protein binding

Cellular Component

endoplasmic reticulum
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000358024
Coding exons: 5
Length: 45168
Individuals with no LoFs: 125730
Homozygous LoFs: 0
Heterozygous LoFs: 13
Defined: 125743
p: 0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.23	338	475	0.712	0.0000332	4589
Missense (PolyPhen)		89	158.27	0.56235		1490
Synonymous	-0.196	219	215	1.02	0.0000155	1512
Loss of Function	3.27	5	21.3	0.235	9.19e-7	244

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00019	0.00018	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.000038	0.000035	rare
South Asian	0	0.0	absent
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be involved in the regulation of the proteolytic processing of the amyloid precursor protein (APP) possibly also implicating APOE. {ECO:0000269|PubMed:21593558}.;

Recessive Scores

pRec: 0.111

Intolerance Scores

LoFtool: 0.216
RVIS EVS: -1.06
RVIS percentile EVS: 7.48

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.619

Gene Damage Prediction

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