Is TECPR2 p.Val81fs (c.242_243del) pathogenic?

TECPR2 p.Val81fs (c.242243del) is classified Pathogenic in TECPR2 (ClinVar, Single submitter, 1 submitter; last evaluated 2016-01-22). No gnomAD frequency available for this variant.

How common is TECPR2 p.Val81fs (c.242_243del) in the general population?

TECPR2 p.Val81fs (c.242_243del) is no gnomAD frequency available for this variant (gnomAD).

TECPR2 p.Val81fs

c.242_243del · rs886043167 · VCV285656

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 3 of 20
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 5.8	GERP 1.9, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: TECPR2
Protein: p.Val81fs
Coding: c.242_243del
MANE Select: NM_014844
dbSNP: rs886043167
Type: Microsatellite
Location: chr14:102407358 (GRCh38)
Gene constraint: LOEUF 0.607 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 68.27

Full TECPR2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

TECPR2 p.Val81= Likely benign ★ same residue
TECPR2 p.Glu12fs Pathogenic/Likely pathogenic ★★ same type
TECPR2 p.Leu225_Cys226insTer Pathogenic/Likely pathogenic ★★ same type
TECPR2 p.Thr649fs Pathogenic/Likely pathogenic ★★ same type
TECPR2 p.Lys471del Uncertain significance ★★ same type
TECPR2 c.2578+10CCCGCTCCCTGCT[3] Likely benign ★★ same type
TECPR2 c.2578+30_2578+42del Benign ★★ same type
TECPR2 p.Lys471dup Likely benign ★★ same type

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-val81fs (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown