TMEM260

protein-coding

transmembrane protein 260

Gene summary

Enables dolichyl-phosphate-mannose-protein mannosyltransferase activity. Involved in protein maturation. Is active in endoplasmic reticulum membrane. Implicated in T-cell non-Hodgkin lymphoma; non-Hodgkin lymphoma; and stomach cancer. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C14orf101

MANE transcript

NM_017799.4

Inheritance

ClinVar variants

P:40U:139B:24

Top phenotype

Structural heart defects and renal anomalies syndrome

gnomAD constraint

pLI —, LoF o/e 0.83

Max pathogenic AF

—

Genomic locus

chr14:56,488,354-56,650,606

External References & Databases

Ensembl (ENSG00000070269)

Transcript & Mutation Effects

hg38 • Region Span ~162.3 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

structural heart defects and renal anomalies syndromeSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0044321

Submitter: Labcorp Genetics (formerly Invitae)

structural heart defects and renal anomalies syndromeSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0044321

Submitter: G2P

structural heart defects and renal anomalies syndromeSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0044321

Submitter: PanelApp Australia

Clinical Genomic Database (CGD)

Structural heart defects and renal anomalies syndromeAR

Manifestation: Cardiovascular; Neurologic; Renal

Intervention: Cardiovascular

Rationale: The condition can involve congenital cardiac anomalies, and awareness may allow early management

Refs: 28318500; 34612517

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TMEM260 variants in ClinVar

6 Conditions Cataloged

Inborn genetic diseasesTotal: 129

Structural heart defects and renal anomalies syndromeTotal: 45

not providedTotal: 34

TMEM260-related disorderTotal: 21

not specifiedTotal: 3

Type I truncus arteriosusTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_017799.4. 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			3 clinvar	12 clinvar	2 clinvar	17
missense	1 clinvar	2 clinvar	131 clinvar	9 clinvar	1 clinvar	144
nonsense	2 clinvar	6 clinvar				8
start loss						0
frameshift	7 clinvar	16 clinvar				23
splice donor/acceptor (+/-2bp)	2 clinvar	4 clinvar	5 clinvar			11
Total	12	28	139	21	3	203

Highest pathogenic variant AF is 0.000120335004

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 51 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_017799.4	RefSeq	NP_060269.3	16	MANE Select
ENST00000261556.11	Ensembl	ENSP00000261556.6	16	MANE Select
ENST00000538838.5	Ensembl	ENSP00000441934.1	11	Standard
ENST00000538838.6	Ensembl	ENSP00000441934.1	11	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
tmem260	Danio rerio	Structure: proximal convoluted tubule Quality: morphology abnormal

Gene / Model

Organism

Observed Phenotype

tmem260

Danio rerio

Structure: proximal convoluted tubule

Quality: morphology

abnormal

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: ENST00000261556
Coding exons: 16
Length: 162253
Individuals with no LoFs: 125612
Homozygous LoFs: 0
Heterozygous LoFs: 136
Defined: 125748
p: 0.000541

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.741	397	358	1.11	0.0000184	4577
Missense (PolyPhen)		103	97.669	1.0546		1198
Synonymous	-0.774	142	131	1.09	0.00000721	1373
Loss of Function	0.962	32	38.4	0.833	0.00000192	465

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00062	0.00062	rare
Latino/Admixed American	0.00033	0.00032	rare
Ashkenazi Jewish	0.0021	0.0020	notable
East Asian	0.00054	0.00054	rare
Finnish	0.00018	0.00018	rare
European (Non-Finnish)	0.00054	0.00053	rare
South Asian	0.00049	0.00049	rare
Other	0.00099	0.00098	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

RVIS EVS: -0.55
RVIS percentile EVS: 19.93

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N

Gene Damage Prediction

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