TMEM44

protein-coding

transmembrane protein 44

Gene summary

Predicted to enable basic amino acid transmembrane transporter activity. Predicted to be involved in basic amino acid transmembrane transport. Predicted to be located in membrane. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001011655.3

Inheritance

—

ClinVar variants

U:97B:9

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.02

Max pathogenic AF

—

Genomic locus

chr3:194,587,673-194,633,689

External References & Databases

Ensembl (ENSG00000145014)

Transcript & Mutation Effects

hg38 • Region Span ~46.0 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 TMEM44 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 97

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001011655.3. 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			2 clinvar	6 clinvar		8
missense			91 clinvar	3 clinvar		94
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	97	9	0	106

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_001011655.3	RefSeq	NP_001011655.1	10	MANE Select
ENST00000347147.9	Ensembl	ENSP00000333355.6	10	MANE Select
NM_001166305.2	RefSeq	NP_001159777.1	11	Standard
NM_001166306.2	RefSeq	NP_001159778.1	10	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: ENST00000392432
Coding exons: 11
Length: 46017
Individuals with no LoFs: 125659
Homozygous LoFs: 1
Heterozygous LoFs: 88
Defined: 125748
p: 0.000354

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.300	273	259	1.05	0.0000154	2965
Missense (PolyPhen)		89	75.78	1.1745		752
Synonymous	-0.831	121	110	1.10	0.00000663	995
Loss of Function	-0.0892	23	22.5	1.02	0.00000113	250

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00013	0.00012	rare
Latino/Admixed American	0.00050	0.00049	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00016	0.00016	rare
Finnish	0.000047	0.000046	rare
European (Non-Finnish)	0.00025	0.00025	rare
South Asian	0.0012	0.0011	notable
Other	0.00050	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0933

Intolerance Scores

LoFtool: 0.981
RVIS EVS: 1.78
RVIS percentile EVS: 96.84

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.117

Gene Damage Prediction

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