TECPR2 p.Ser978=
c.2934C>T · rs766701687 · VCV2200657
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0165%, mid)
Conditions
2
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.97 | GERP -3, phastCons 0.006 |
| Overall | ||
| CADD | 5.194 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0165%
Middle Eastern · 1/6,074 alleles
Filtering AF
0.00324%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00207%
Overall
0.00149%
24/1,613,070 alleles · ultra-rare
exomes 22/1,461,112 · genomes 2/151,958 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0165% | 6,074 |
| East Asian | 0.00892% | 11,213 |
| Admixed American | 0.00835% | 11,980 |
| African / African-American | 0.00267% | 37,402 |
| European (non-Finnish) | 0.00102% | 98,294 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- TECPR2
- Protein
- p.Ser978=
- Coding
- c.2934C>T
- MANE Select
- NM_014844
- dbSNP
- rs766701687
- Type
- single nucleotide variant
- Location
- chr14:102445806 (GRCh38)
- Gene constraint
- LOEUF 0.607 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 68.27
Similar variants
- TECPR2 c.1084+2T>C Likely pathogenic ★★ same condition
- TECPR2 c.1418-2A>G Likely pathogenic ★★ same condition
- TECPR2 c.2753-1G>A Likely pathogenic ★★ same condition
- TECPR2 p.Gln1189Ter Pathogenic/Likely pathogenic ★★ same condition
- TECPR2 p.Gln191Ter Pathogenic/Likely pathogenic ★★ same condition
- TECPR2 p.Gln852Ter Pathogenic ★★ same condition
- TECPR2 p.Trp1024Ter Pathogenic ★★ same condition
- TECPR2 p.Trp1288Ter Pathogenic/Likely pathogenic ★★ same condition
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/tecpr2-p-ser978 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown