GeneBe

LTV1

protein-coding

LTV1 ribosome biogenesis factor, the group of SSU processome

Gene summary

Predicted to be involved in ribosomal small subunit biogenesis and ribosomal small subunit export from nucleus. Located in cytosol and nucleoplasm. Implicated in inflammatory poikiloderma with hair abnormalities and acral keratoses. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:
  • C6orf93

MANE transcript

NM_032860.5

Inheritance

AR

ClinVar variants

P:1U:64B:6

Top phenotype

Inflammatory poikiloderma with hair abnormalities and acral keratoses

gnomAD constraint

pLI —, LoF o/e 0.57

Max pathogenic AF

—

Genomic locus

chr6:143,843,338-143,863,812

External References & Databases

Ensembl (ENSG00000135521)NCBI Gene (84946)OMIM (620074)HGNC:21173GenCCUniProt (Q96GA3)AlphaFoldClinVar (LTV1)gnomADPubMedJAXSFARI

Transcript & Mutation Effects

hg38 • Region Span ~20.5 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

inflammatory poikiloderma with hair abnormalities and acral keratosesLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0859355

Submitter: G2P

inflammatory poikiloderma with hair abnormalities and acral keratosesLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0859355

Submitter: Ambry Genetics

inflammatory poikiloderma with hair abnormalities and acral keratosesLIMITED

Inheritance Pattern: Unknown

Disease ID:MONDO:0859355

Submitter: Labcorp Genetics (formerly Invitae)

inflammatory poikiloderma with hair abnormalities and acral keratosesMODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0859355

Submitter: PanelApp Australia

Clinical Genomic Database (CGD)

Inflammatory poikiloderma with hair abnormalities and acral keratosesAR

Manifestation: Dermatologic

Intervention: General

Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing

Refs: 34999892Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to LTV1 variants in ClinVar

3 Conditions Cataloged
not specifiedTotal: 61
not providedTotal: 5
Inflammatory poikiloderma with hair abnormalities and acral keratosesTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_032860.5. 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.

EffectPLPVUSLBBSum
synonymous
2
clinvar
1
clinvar
2
clinvar
 5
missense
1
clinvar
60
clinvar
2
clinvar
1
clinvar
 64
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
2
clinvar
 2
Total10643371

Highest pathogenic variant AF is 0.000028731347

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 16 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_032860.5RefSeqNP_116249.211MANE Select
ENST00000367576.6EnsemblENSP00000356548.511MANE Select
NM_001329953.2RefSeqNP_001316882.17Standard
ENST00000868801.1EnsemblENSP00000538860.111Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
ltv1Danio rerio

Structure: head

Quality: decreased width

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

  • ribosomal small subunit export from nucleus
  • ribosomal small subunit biogenesis

Molecular Function

  • protein binding

Cellular Component

  • nucleus
  • nucleoplasm
  • cytosol
  • preribosome, small subunit precursor
  • late endosome membrane

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000367576
Coding exons
11
Length
20469
Individuals with no LoFs
125541
Homozygous LoFs
0
Heterozygous LoFs
207
Defined
125748
p
0.000823
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.4392252440.9210.00001193158
Missense (PolyPhen)7186.0130.825451079
Synonymous0.9627687.40.8690.00000429827
Loss of Function2.101628.00.5720.00000159339

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000620.00062rare
Latino/Admixed American0.000490.00049rare
Ashkenazi Jewish00.0absent
East Asian0.000330.00033rare
Finnish0.000230.00023rare
European (Non-Finnish)0.00120.0012notable
South Asian0.000790.00078rare
Other0.00130.0013notable

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec
0.0955

Intolerance Scores

LoFtool
0.317
RVIS EVS
0.17
RVIS percentile EVS
65.96

Essentials

Essential (CRISPR)
E
Essential (CRISPR2)
E
Essential (gene trap)
E
Indispensability pred.
N
Indispensability score
0.186

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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