CCSER1

coiled-coil serine rich protein 1

Basic information

Region (hg38): 4:90127393-91605295

Previous symbols: [ "FAM190A" ]

Links

ENSG00000184305 ∙ NCBI:401145 ∙ OMIM:618934 ∙ HGNC:29349 ∙ Uniprot:Q9C0I3 ∙ 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 CCSER1 gene.

• Inborn genetic diseases (35 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCSER1 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			33	2	1	36
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	33	3	1

Variants in CCSER1

This is a list of pathogenic ClinVar variants found in the CCSER1 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-90308291-G-C		not specified	Uncertain significance (Dec 07, 2023)
4-90308324-C-T		not specified	Uncertain significance (Jun 08, 2022)
4-90308397-C-T		not specified	Uncertain significance (Feb 21, 2024)
4-90308527-G-C		not specified	Uncertain significance (Feb 07, 2023)
4-90308645-A-G		not specified	Uncertain significance (Jan 30, 2024)
4-90308661-A-C		not specified	Uncertain significance (Feb 02, 2022)
4-90308964-C-T		not specified	Uncertain significance (Jun 17, 2022)
4-90308994-G-A		not specified	Uncertain significance (Mar 07, 2024)
4-90308997-C-T		not specified	Uncertain significance (Feb 28, 2023)
4-90309041-A-G		not specified	Uncertain significance (May 25, 2022)
4-90309146-G-A		not specified	Uncertain significance (Jul 05, 2022)
4-90309216-C-G		not specified	Uncertain significance (Dec 14, 2023)
4-90309216-C-T		not specified	Likely benign (Jul 14, 2023)
4-90309222-C-T		not specified	Uncertain significance (Jun 30, 2023)
4-90309258-G-A		not specified	Uncertain significance (Jun 22, 2021)
4-90309293-T-C			Likely benign (Oct 01, 2022)
4-90309297-C-T		not specified	Uncertain significance (Sep 16, 2021)
4-90309353-G-A		not specified	Uncertain significance (Apr 26, 2023)
4-90309582-A-G		not specified	Uncertain significance (Oct 29, 2021)
4-90309603-C-T		not specified	Uncertain significance (Oct 18, 2021)
4-90312889-C-T		not specified	Uncertain significance (Aug 17, 2022)
4-90312974-A-G		not specified	Uncertain significance (Jun 06, 2023)
4-90313012-A-G		not specified	Uncertain significance (Jul 19, 2022)
4-90400094-T-G		not specified	Uncertain significance (Dec 03, 2021)
4-90468279-T-C		not specified	Uncertain significance (Nov 19, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCSER1	protein_coding	protein_coding	ENST00000509176	10	1474379

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000789	0.999	124616	0	20	124636	0.0000802

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.12	397	465	0.854	0.0000239	5857
Missense in Polyphen		127	168.89	0.75198		2310
Synonymous	0.286	170	175	0.973	0.00000944	1764
Loss of Function	3.64	12	35.4	0.339	0.00000196	471

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000228	0.000221
Ashkenazi Jewish	0.000201	0.000199
East Asian	0.000112	0.000111
Finnish	0.00	0.00
European (Non-Finnish)	0.0000903	0.0000885
Middle Eastern	0.000112	0.000111
South Asian	0.0000376	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.82
• rvis_percentile_EVS: 88.07

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.372

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• 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: Ccser1