Is TEX14 p.Ile367= (c.1101C>T) pathogenic?

TEX14 p.Ile367= (c.1101C>T) is classified Likely benign in TEX14 (ClinVar, Single submitter, 1 submitter; last evaluated 2018-07-25). Ultra-rare (popmax 0.0487%, nfe).

How common is TEX14 p.Ile367= (c.1101C>T) in the general population?

TEX14 p.Ile367= (c.1101C>T) is ultra-rare (popmax 0.0487%, nfe) (gnomAD).

TEX14 p.Ile367=

c.1101C>T · rs192936672 · VCV732499

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0487%, nfe)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 3.1	GERP -0.97, phastCons 1
Overall
CADD	8.089	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0487% European (non-Finnish) · 574/1,179,644 alleles

Filtering AF 0.0453% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.044%

Overall 0.0368% 594/1,613,646 alleles · ultra-rare exomes 567/1,461,486 · genomes 27/152,160 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0487%	2,055
Remaining individualsnot grpmax-eligible	0.0144%	6,944
African / African-American	0.0107%	9,375
Admixed American	0.005%	19,999

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: TEX14
Protein: p.Ile367=
Coding: c.1101C>T
MANE Select: NM_031272
dbSNP: rs192936672
Type: single nucleotide variant
Location: chr17:58611244 (GRCh38)
Gene constraint: LOEUF 1.043 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 50.95 · 2 PDB
Residue 367: the protein kinase domain

Full TEX14 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

TEX14 p.Ile367Ser Uncertain significance ★ ⚠ same residue
TEX14 p.Glu1351Gly Uncertain significance ★★ ⚠ same type
TEX14 c.2789-7T>C Benign ★★ same type
TEX14 c.3717+7A>G Likely benign ★★ same type
TEX14 p.Leu1380Phe Benign/Likely benign ★★ same type
TEX14 p.Thr979= Benign ★★ same type
TEX14 c.4267+1G>A Likely pathogenic ★ same type
TEX14 p.Arg1218Ter Likely pathogenic ★ 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/tex14-p-ile367 (accessed [today's date]).

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