SYNDIG1L

synapse differentiation inducing 1 like, the group of interferon induced transmembrane protein domain containing

Basic information

Region (hg38): 14:74405894-74426210

Previous symbols: [ "TMEM90A" ]

Links

ENSG00000183379 ∙ NCBI:646658 ∙ OMIM:609999 ∙ HGNC:32388 ∙ Uniprot:A6NDD5 ∙ 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 SYNDIG1L gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SYNDIG1L 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						0
missense			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	0	0

Variants in SYNDIG1L

This is a list of pathogenic ClinVar variants found in the SYNDIG1L region.

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

Position	Type	Phenotype	Significance	ClinVar
14-74407575-A-G		not specified	Uncertain significance (Jan 22, 2024)
14-74407609-C-T		not specified	Uncertain significance (Dec 28, 2022)
14-74407638-C-T		not specified	Uncertain significance (Jan 27, 2022)
14-74407929-C-T		not specified	Uncertain significance (Oct 27, 2022)
14-74409384-A-G		not specified	Uncertain significance (Apr 12, 2024)
14-74409411-C-A		not specified	Uncertain significance (Oct 25, 2022)
14-74409475-G-T		not specified	Uncertain significance (May 03, 2023)
14-74409668-G-A		not specified	Uncertain significance (Nov 12, 2021)
14-74409671-T-C		not specified	Uncertain significance (Feb 22, 2023)
14-74409681-G-A		not specified	Uncertain significance (Jan 08, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SYNDIG1L	protein_coding	protein_coding	ENST00000331628	3	20210

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00879	0.816	125553	0	7	125560	0.0000279

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.213	124	131	0.948	0.00000750	1522
Missense in Polyphen		57	58.283	0.97799		675
Synonymous	-0.344	60	56.7	1.06	0.00000339	504
Loss of Function	1.07	4	7.07	0.566	3.01e-7	90

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000117	0.000117
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000558	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000179	0.0000176
Middle Eastern	0.0000558	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.57
• rvis_percentile_EVS: 81.99

Haploinsufficiency Scores

• pHI: 0.141
• hipred: N
• hipred_score: 0.345
• ghis: 0.408

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Syndig1l

Gene ontology

• Cellular component: Golgi apparatus;integral component of membrane