CLTRN

collectrin, amino acid transport regulator

Basic information

Region (hg38): X:15627318-15675012

Previous symbols: [ "TMEM27" ]

Links

ENSG00000147003

∙ NCBI:57393 ∙ OMIM:300631 ∙ HGNC:29437 ∙ Uniprot:Q9HBJ8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

Hartnup disease (Supportive), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CLTRN gene.

not_specified (24 variants)
Autism (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLTRN gene is commonly pathogenic or not. These statistics are base on transcript: NM_000020665.6. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			22 clinvar	2 clinvar		24
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	22	2	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CLTRN	protein_coding	protein_coding	ENST00000380342	6	37714

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000113	0.389	125678	9	32	125719	0.000163

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.279	81	74.2	1.09	0.00000513	1465
Missense in Polyphen		25	19.647	1.2725		432
Synonymous	0.824	20	25.3	0.791	0.00000173	417
Loss of Function	0.0861	6	6.23	0.963	3.93e-7	126

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00103	0.00103
Ashkenazi Jewish	0.000144	0.0000992
East Asian	0.0000745	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000745	0.0000528
Middle Eastern	0.0000745	0.0000544
South Asian	0.000106	0.0000653
Other	0.000668	0.000489

dbNSFP

Source: dbNSFP

Function: FUNCTION: Regulator of SNARE complex function. Stimulator of beta cell replication. {ECO:0000269|PubMed:16330323}.;

Recessive Scores

pRec: 0.109

Intolerance Scores

loftool
rvis_EVS: -0.19
rvis_percentile_EVS: 39.68

Haploinsufficiency Scores

pHI: 0.870
hipred: N
hipred_score: 0.253
ghis: 0.452

Essentials

essential_gene_CRISPR
essential_gene_CRISPR2
essential_gene_gene_trap: N
gene_indispensability_pred
gene_indispensability_score

Mouse Genome Informatics

Gene name: Cltrn
Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); renal/urinary system phenotype; muscle phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype; cellular phenotype; homeostasis/metabolism phenotype;