TEX55

protein-coding

testis expressed 55

Gene summary

Located in sperm flagellum. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C3orf30

MANE transcript

NM_152539.3

Inheritance

—

ClinVar variants

U:7

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.78

Max pathogenic AF

—

Genomic locus

chr3:119,146,151-119,160,042

External References & Databases

Ensembl (ENSG00000163424)

Transcript & Mutation Effects

hg38 • Region Span ~13.9 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 TEX55 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 7

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_152539.3. 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						0
missense			7 clinvar			7
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	7	0	0	7

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 7 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_152539.3	RefSeq	NP_689752.2	3	MANE Select
ENST00000295622.6	Ensembl	ENSP00000295622.1	3	MANE Select
ENST00000460150.1	Ensembl	ENSP00000418207.1	2	Standard
ENST00000473121.1	Ensembl	ENSP00000419675.1	3	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000295622
Coding exons: 3
Length: 13893
Individuals with no LoFs: 124345
Homozygous LoFs: 0
Heterozygous LoFs: 2
Defined: 124347
p: 0.00000804

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.00346	288	288	0.999	0.0000145	3531
Missense (PolyPhen)		99	105.12	0.94175		1355
Synonymous	1.22	92	108	0.851	0.00000575	1026
Loss of Function	0.916	15	19.3	0.775	0.00000101	225

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.0000090	0.0000088	rare
South Asian	0	0.0	absent
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.973
RVIS EVS: 3.2
RVIS percentile EVS: 99.34

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	High
Cancer	Medium	Medium	Medium