TMEM72

protein-coding

transmembrane protein 72

Gene summary

This gene encodes a transmembrane protein which may be expressed specifically in the kidney. [provided by RefSeq, Sep 2016]

Previous symbols:

C10orf127

MANE transcript

NM_001123376.3

Inheritance

—

ClinVar variants

U:4B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.11

Max pathogenic AF

—

Genomic locus

chr10:44,911,316-44,937,010

External References & Databases

Ensembl (ENSG00000187783)

Transcript & Mutation Effects

hg38 • Region Span ~25.7 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 TMEM72 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 3

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001123376.3. 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			1
missense			3 clinvar	1 clinvar		4
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	4	1	0	5

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 8 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001123376.3	RefSeq	NP_001116848.1	5	MANE Select
ENST00000389583.5	Ensembl	ENSP00000374234.4	5	MANE Select
NM_001345926.2	RefSeq	NP_001332855.1	1	Standard
ENST00000544540.5	Ensembl	ENSP00000439911.1	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000389583
Coding exons: 5
Length: 25803
Individuals with no LoFs: 124545
Homozygous LoFs: 0
Heterozygous LoFs: 38
Defined: 124583
p: 0.000153

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0656	153	155	0.985	0.00000830	1759
Missense (PolyPhen)		41	51.854	0.79069		599
Synonymous	0.329	67	70.5	0.950	0.00000412	584
Loss of Function	2.54	1	9.42	0.106	3.99e-7	115

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00013	0.00013	rare
Latino/Admixed American	0.00090	0.00090	rare
Ashkenazi Jewish	0.00010	0.00010	rare
East Asian	0.000056	0.000056	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000027	0.000027	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.203
RVIS EVS: -0.2
RVIS percentile EVS: 38.82

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.125

Gene Damage Prediction

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