CCSER2

coiled-coil serine rich protein 2

Basic information

Region (hg38): 10:84328586-84518521

Previous symbols: [ "KIAA1128", "FAM190B" ]

Links

ENSG00000107771 ∙ NCBI:54462 ∙ OMIM:619944 ∙ HGNC:29197 ∙ Uniprot:Q9H7U1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CCSER2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCSER2 gene is commonly pathogenic or not.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			43	1		44
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			4			4
Total	0	0	47	2	0

Variants in CCSER2

This is a list of pathogenic ClinVar variants found in the CCSER2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
10-84371078-C-G		not specified	Uncertain significance (Aug 13, 2021)
10-84371117-C-T		not specified	Uncertain significance (Apr 22, 2022)
10-84371179-A-G		not specified	Uncertain significance (Apr 08, 2024)
10-84371195-A-G		not specified	Uncertain significance (Dec 30, 2023)
10-84371203-A-G		not specified	Uncertain significance (Jan 26, 2023)
10-84371297-C-T		not specified	Uncertain significance (Nov 09, 2021)
10-84371426-C-G		not specified	Uncertain significance (Feb 06, 2024)
10-84371431-C-T		not specified	Uncertain significance (Oct 17, 2023)
10-84371437-A-G		not specified	Uncertain significance (Sep 16, 2021)
10-84371552-A-G		not specified	Likely benign (Sep 01, 2021)
10-84371620-G-A		not specified	Uncertain significance (Nov 09, 2023)
10-84371662-G-A		not specified	Uncertain significance (May 13, 2024)
10-84371672-C-A		not specified	Uncertain significance (Dec 21, 2022)
10-84371731-T-A		not specified	Uncertain significance (Apr 08, 2024)
10-84371755-C-G		not specified	Uncertain significance (Oct 29, 2021)
10-84371762-C-G		not specified	Uncertain significance (Jul 14, 2021)
10-84371768-C-T		not specified	Uncertain significance (Apr 26, 2023)
10-84371825-A-G		not specified	Uncertain significance (Dec 06, 2021)
10-84371893-A-G		not specified	Uncertain significance (Jul 25, 2023)
10-84371894-A-G		not specified	Uncertain significance (Dec 09, 2023)
10-84371986-A-G		not specified	Uncertain significance (Sep 26, 2022)
10-84371998-A-G		not specified	Uncertain significance (Aug 02, 2021)
10-84372052-A-G		not specified	Uncertain significance (May 18, 2022)
10-84372068-A-C		not specified	Uncertain significance (Nov 10, 2022)
10-84372326-A-G		not specified	Uncertain significance (Sep 15, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCSER2	protein_coding	protein_coding	ENST00000224756	10	189932

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.667	0.333	125718	0	20	125738	0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0727	432	428	1.01	0.0000207	5517
Missense in Polyphen		141	147.09	0.9586		2030
Synonymous	-0.406	159	153	1.04	0.00000723	1540
Loss of Function	4.32	7	34.3	0.204	0.00000179	465

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000360	0.000359
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000708	0.0000703
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000654	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Microtubule-binding protein which might play a role in microtubule bundling. {ECO:0000250|UniProtKB:Q3UHI0}.

Recessive Scores

• pRec: 0.0941

Intolerance Scores

• rvis_EVS: 0.45
• rvis_percentile_EVS: 77.98

Haploinsufficiency Scores

• pHI: 0.129
• hipred: N
• hipred_score: 0.328
• ghis: 0.494

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccser2

Gene ontology

• Biological process: microtubule bundle formation
• Cellular component: cytoplasm;microtubule cytoskeleton
• Molecular function: microtubule binding