rs786201030

Variant names:

• chr22-24322169-A-C
• rs786201030
• NM_015330.6:c.1189A>C

Variant summary

Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM1 PM2 PP5_Moderate

The NM_015330.6(SPECC1L):​c.1189A>C​(p.Thr397Pro) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: SPECC1L NM_015330.6 missense
• Clinical Significance: Pathogenic criteria provided, single submitter P:3
• Conservation: PhyloP100: 9.12

Genes affected

SPECC1L (HGNC:29022): (sperm antigen with calponin homology and coiled-coil domains 1 like) This gene encodes a coiled-coil domain containing protein. The encoded protein may play a critical role in actin-cytoskeletal reorganization during facial morphogenesis. Mutations in this gene are a cause of oblique facial clefting-1. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. A read-through transcript composed of SPECC1L (sperm antigen with calponin homology and coiled-coil domains 1-like) and the downstream ADORA2A (adenosine A2a receptor) gene sequence has been identified, but it is thought to be non-coding. [provided by RefSeq, Jun 2013]

SPECC1L-ADORA2A (HGNC:49185): (SPECC1L-ADORA2A readthrough (NMD candidate)) This locus represents naturally occurring readthrough transcription between the neighboring SPECC1L (sperm antigen with calponin homology and coiled-coil domains 1-like) and ADORA2A (adenosine A2a receptor) genes on chromosome 22. The readthrough transcript is a candidate for nonsense-mediated mRNA decay (NMD) and is unlikely to produce a protein product. [provided by RefSeq, Jun 2013]

ACMG classification

Verdict is Likely_pathogenic. Variant got 6 ACMG points.

• PM1: In a coiled_coil_region (size 55) in uniprot entity CYTSA_HUMAN there are 4 pathogenic changes around while only 0 benign (100%) in NM_015330.6
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 22-24322169-A-C is Pathogenic according to our data. Variant chr22-24322169-A-C is described in ClinVar as [Pathogenic]. Clinvar id is 183671.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-24322169-A-C is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPECC1L	NM_015330.6	c.1189A>C	p.Thr397Pro	missense_variant	Exon 5 of 17	ENST00000314328.14	NP_056145.5
SPECC1L	NM_001145468.4	c.1189A>C	p.Thr397Pro	missense_variant	Exon 4 of 16		NP_001138940.4
SPECC1L	NM_001254732.3	c.1189A>C	p.Thr397Pro	missense_variant	Exon 4 of 15		NP_001241661.3
SPECC1L-ADORA2A	NR_103546.1	n.1497A>C		non_coding_transcript_exon_variant	Exon 5 of 20

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPECC1L	ENST00000314328.14	c.1189A>C	p.Thr397Pro	missense_variant	Exon 5 of 17	1	NM_015330.6	ENSP00000325785.8
SPECC1L-ADORA2A	ENST00000358654.2	n.1189A>C		non_coding_transcript_exon_variant	Exon 5 of 20	2		ENSP00000351480.2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 33

Alfa AF: 0.0000936 Hom.: 0

Bravo AF: 0.00000756

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:3

Revision: criteria provided, single submitter

Submissions by phenotype

Teebi hypertelorism syndrome Pathogenic:1

Jun 01, 2018

Dept of Genetics, Assistance Publique-Hôpitaux de Paris (APHP) - R DEBRE University Hospital

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Teebi hypertelorism syndrome 1 Pathogenic:1

Feb 01, 2015

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

- -

not provided Pathogenic:1

Feb 01, 2023

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is not present in population databases (gnomAD no frequency). For these reasons, this variant has been classified as Pathogenic. Experimental studies have shown that this missense change affects SPECC1L function (PMID: 25412741). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). ClinVar contains an entry for this variant (Variation ID: 183671). This missense change has been observed in individual(s) with clinical features of SPECC1L-related disorders (PMID: 25412741, 30472488). It has also been observed to segregate with disease in related individuals. This sequence change replaces threonine, which is neutral and polar, with proline, which is neutral and non-polar, at codon 397 of the SPECC1L protein (p.Thr397Pro). -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.98
BayesDel_addAF	Pathogenic	0.22	D
BayesDel_noAF	Uncertain	0.080
CADD	Pathogenic	29
DANN	Uncertain	1.0
Eigen	Pathogenic	0.80
Eigen_PC	Pathogenic	0.77
FATHMM_MKL	Uncertain	0.96	D
LIST_S2	Uncertain	0.95	.;D;.;.
M_CAP	Uncertain	0.091	D
MetaRNN	Uncertain	0.69	D;D;D;D
MetaSVM	Benign	-1.1	T
PrimateAI	Pathogenic	0.81	D
PROVEAN	Uncertain	-3.1	D;D;D;D
REVEL	Pathogenic	0.80
Sift	Uncertain	0.0010	D;D;D;D
Sift4G	Uncertain	0.011	D;D;D;D
Vest4		0.87
MutPred		0.18		Loss of catalytic residue at T397 (P = 0.075);Loss of catalytic residue at T397 (P = 0.075);Loss of catalytic residue at T397 (P = 0.075);Loss of catalytic residue at T397 (P = 0.075);
MVP		0.57
MPC		1.4
ClinPred		0.96	D
GERP RS		5.4
gMVP		0.72

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs786201030; hg19: chr22-24718137;