SCAMP4

secretory carrier membrane protein 4, the group of Secretory carrier membrane proteins

Basic information

Region (hg38): 19:1905213-1926013

Links

ENSG00000227500 ∙ NCBI:113178 ∙ OMIM:613764 ∙ HGNC:30385 ∙ Uniprot:Q969E2 ∙ 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 SCAMP4 gene.

• Inborn genetic diseases (40 variants)
• not provided (35 variants)
• Intellectual disability-strabismus syndrome (22 variants)
• not specified (17 variants)
• Intellectual disability (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCAMP4 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			9	4		13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding		2	60	14	7	83
Total	0	2	69	19	7

Highest pathogenic variant AF is 0.0000920

Variants in SCAMP4

This is a list of pathogenic ClinVar variants found in the SCAMP4 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-1912063-C-T			Uncertain significance (Nov 30, 2016)
19-1912069-TGTCTCCCACAGTCG-T			Likely pathogenic (Nov 03, 2020)
19-1912083-G-A			Likely benign (Feb 28, 2018)
19-1912101-G-C		Intellectual disability-strabismus syndrome	Uncertain significance (Aug 08, 2019)
19-1912103-C-T		Inborn genetic diseases	Uncertain significance (Apr 12, 2023)
19-1912106-C-T		not specified • Intellectual disability-strabismus syndrome	Uncertain significance (Oct 05, 2018)
19-1912109-C-G		not specified	Uncertain significance (Jan 18, 2017)
19-1912114-C-T		not specified	Uncertain significance (Dec 29, 2017)
19-1912125-G-T		Inborn genetic diseases	Uncertain significance (Jan 07, 2022)
19-1912134-C-G		Inborn genetic diseases	Uncertain significance (Aug 02, 2023)
19-1912141-G-GCCGGGAGC		Intellectual disability-strabismus syndrome	Pathogenic (Sep 10, 2021)
19-1912155-G-C		Inborn genetic diseases	Uncertain significance (Nov 09, 2022)
19-1912158-T-G			Likely benign (Apr 01, 2023)
19-1912163-C-T		Inborn genetic diseases	Uncertain significance (Jun 18, 2021)
19-1912164-G-A			Benign/Likely benign (Apr 01, 2024)
19-1912165-G-T		Inborn genetic diseases	Uncertain significance (Sep 29, 2023)
19-1912194-C-T			Likely benign (Jan 01, 2024)
19-1912198-A-C		Inborn genetic diseases	Likely benign (Feb 17, 2022)
19-1912208-G-A		Inborn genetic diseases	Uncertain significance (Aug 02, 2023)
19-1912228-G-T		Inborn genetic diseases	Conflicting classifications of pathogenicity (Jan 01, 2024)
19-1912262-C-T		Inborn genetic diseases	Uncertain significance (Nov 03, 2022)
19-1912263-C-G			Benign (Dec 31, 2019)
19-1912298-C-G		Inborn genetic diseases	Uncertain significance (Sep 16, 2021)
19-1912305-C-T			Likely benign (Dec 31, 2019)
19-1912321-A-C			Uncertain significance (Apr 14, 2017)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SCAMP4	protein_coding	protein_coding	ENST00000316097	6	20804

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00457	0.968	124611	0	18	124629	0.0000722

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.201	139	146	0.953	0.00000967	1477
Missense in Polyphen		52	58.832	0.88387		687
Synonymous	-1.19	80	67.6	1.18	0.00000532	432
Loss of Function	1.93	6	13.7	0.438	6.64e-7	131

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000293	0.000287
Ashkenazi Jewish	0.000101	0.0000994
East Asian	0.000111	0.000111
Finnish	0.00	0.00
European (Non-Finnish)	0.0000825	0.0000797
Middle Eastern	0.000111	0.000111
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probably involved in membrane protein trafficking. {ECO:0000250}.

Recessive Scores

• pRec: 0.101

Intolerance Scores

• loftool: 0.677
• rvis_EVS: 0.22
• rvis_percentile_EVS: 68.27

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.292
• ghis: 0.530

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.236

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Scamp4

Gene ontology

• Biological process: protein transport
• Cellular component: Golgi membrane;Golgi apparatus;integral component of membrane;trans-Golgi network membrane;recycling endosome membrane