SPATC1L spermatogenesis and centriole associated 1 like [Homo sapiens (human)] - Gene

Summary

Official Symbol: SPATC1Lprovided by HGNC
Official Full Name: spermatogenesis and centriole associated 1 likeprovided by HGNC
Primary source: HGNC:HGNC:1298
See related: Ensembl:ENSG00000160284 MIM:612412; AllianceGenome:HGNC:1298
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: C21orf56
Summary: Enables identical protein binding activity. Predicted to act upstream of or within several processes, including actin polymerization or depolymerization; positive regulation of cAMP-dependent protein kinase activity; and positive regulation of protein kinase A signaling. Predicted to be located in sperm connecting piece. Predicted to be active in centrosome. [provided by Alliance of Genome Resources, Apr 2022]
Expression: Broad expression in testis (RPKM 5.7), prostate (RPKM 2.7) and 22 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 21q22.3

Exon count:: 6

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	21	NC_000021.9 (46161160..46184459, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	21	NC_060945.1 (44540975..44566185, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	21	NC_000021.8 (47581074..47604373, complement)

Chromosome 21 - NC_000021.9 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Balanced chromosomal rearrangements implicate YIPF5 and SPATC1L in non-obstructive oligoasthenozoospermia and oligozoospermia and of a derivative chromosome 22 in recurrent miscarriage.
Title: Balanced chromosomal rearrangements implicate YIPF5 and SPATC1L in non-obstructive oligoasthenozoospermia and oligozoospermia and of a derivative chromosome 22 in recurrent miscarriage.
Biallelic mutations in spermatogenesis and centriole-associated 1 like (SPATC1L) cause acephalic spermatozoa syndrome and male infertility.
Title: Biallelic mutations in spermatogenesis and centriole-associated 1 like (SPATC1L) cause acephalic spermatozoa syndrome and male infertility.
PTSD is associated with increased DNA methylation across regions of HLA-DPB1 and SPATC1L.
Title: PTSD is associated with increased DNA methylation across regions of HLA-DPB1 and SPATC1L.
these results implicate the SPATC1L-PKA complex in maintaining the stability of the sperm head-tail junction, thereby revealing a new molecular basis for sperm head-tail integrity.
Title: SPATC1L maintains the integrity of the sperm head-tail junction.
SPATC1L was identified as a candidate gene for early-onset and age-related hearing loss.
Title: Next-generation sequencing identified SPATC1L as a possible candidate gene for both early-onset and age-related hearing loss.
TNFSF13, SPATC1L, SLC22A25 and SALL4 may thus be novel susceptibility loci for atrial fibrillation in the Japanese population
Title: Identification of TNFSF13, SPATC1L, SLC22A25 and SALL4 as novel susceptibility loci for atrial fibrillation by an exome‑wide association study.
rs1465567 of EGFLAM and rs113710653 of SPATC1L may be susceptibility loci for true aortic aneurysm and rs143881017 of RNASE13 may be such a locus for dissecting aortic aneurysm in Japanese individuals.
Title: Identification of EGFLAM, SPATC1L and RNASE13 as novel susceptibility loci for aortic aneurysm in Japanese individuals by exome-wide association studies.

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Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-147567 (e-PCR)
- UniSTS:175881

NoName (e-PCR)
- UniSTS:484393

SHGC-107520 (e-PCR)
- UniSTS:170416

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables molecular_function	ND No biological Data available more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein kinase A regulatory subunit binding	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in actin polymerization or depolymerization	IEA Inferred from Electronic Annotation more info
involved_in biological_process	ND No biological Data available more info
involved_in positive regulation of protein kinase A signaling	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of protein phosphorylation	IEA Inferred from Electronic Annotation more info
involved_in spermatogenesis	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
is_active_in cellular_component	ND No biological Data available more info
is_active_in centrosome	IBA Inferred from Biological aspect of Ancestor more info
is_active_in sperm connecting piece	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: speriolin-like protein

Names: spermatogenesis and centriole-associated protein 1-like protein

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001142854.2 → NP_001136326.1 speriolin-like protein isoform 1

See identical proteins and their annotated locations for NP_001136326.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AK304535, AP001468, AW138006

Consensus CDS

CCDS46653.1

UniProtKB/Swiss-Prot

B4E323, Q52LS9, Q6FIH5, Q6P0L3, Q9H0A9, Q9NSE5

Related

ENSP00000291672.5, ENST00000291672.6

Conserved Domains (2) summary

pfam15058
Location:6 → 153

Speriolin_N; Speriolin N terminus

pfam15059
Location:195 → 340

Speriolin_C; Speriolin C-terminus
NM_032261.5 → NP_115637.3 speriolin-like protein isoform 2

See identical proteins and their annotated locations for NP_115637.3

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks an exon in the 5' coding region, compared to variant 1, which results in the use of a downstream in-frame start codon and a protein (isoform 2) with a shorter N-terminus, compared to isoform 1.

Source sequence(s)

AK304535, AW138006

Consensus CDS

CCDS13732.1

UniProtKB/Swiss-Prot

Q9H0A9

Related

ENSP00000333869.6, ENST00000330205.10

Conserved Domains (1) summary

pfam15059
Location:41 → 186

Speriolin_C; Speriolin C-terminus