Is TRNT1 p.Pro23Val (c.67_68delinsGT) pathogenic?

TRNT1 p.Pro23Val (c.6768delinsGT) is classified Benign in TRNT1 (ClinVar, Single submitter, 1 submitter; last evaluated 2026-01-15). Absent from gnomAD; Associated with congenital sideroblastic anemia-B-cell immunodeficiency-periodic fever-developmental delay syndrome.

How common is TRNT1 p.Pro23Val (c.67_68delinsGT) in the general population?

TRNT1 p.Pro23Val (c.67_68delinsGT) is absent from gnomAD (gnomAD).

TRNT1 p.Pro23Val

Q: What condition is associated with TRNT1 p.Pro23Val (c.67_68delinsGT)?

TRNT1 p.Pro23Val (c.67_68delinsGT) is associated with congenital sideroblastic anemia-B-cell immunodeficiency-periodic fever-developmental delay syndrome (ClinVar).

Q: How is Congenital sideroblastic anemia-B-cell immunodeficiency-periodic fever-developmental delay syndrome inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

c.67_68delinsGT · rs1575035403 · VCV772448

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

congenital sideroblastic anemia-B-cell immunodeficiency-periodic fever-developmental delay syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.59	GERP -2.7, phastCons 0.17
Regional constraint	o/e 1.25	unconstrained · MANE · 19 kb · p 1e-08 · regional, not allelic

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: TRNT1
Protein: p.Pro23Val
Coding: c.67_68delinsGT
MANE Select: NM_182916
dbSNP: rs1575035403
Type: Indel
Location: chr3:3129107 (GRCh38)
Gene constraint: LOEUF 1.232 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 90.00 · 3 PDB
Residue 23: a UniProt-annotated variant site (in)

Full TRNT1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

congenital sideroblastic anemia-B-cell immunodeficiency-periodic fever-developmental delay syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Congenital sideroblastic anemia-B-cell immunodeficiency-periodic fever-developmental delay syndrome (Orphanet):

Inheritance: Autosomal recessive
Onset: Infancy, Neonatal

Similar variants

TRNT1 p.Pro23Leu Likely benign ★ same residue
TRNT1 p.Pro23Ala Benign/Likely benign ★★ same residue
TRNT1 p.Pro23= Benign ★ same residue
TRNT1 p.Lys317Glu Uncertain significance ★ same condition
TRNT1 p.Ser47Ile Uncertain significance ★ same condition
TRNT1 c.1055_1056+5del Pathogenic/Likely pathogenic ★★ same condition
TRNT1 p.Arg190fs Pathogenic ★★ same condition
TRNT1 p.Arg190Ile 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/trnt1-p-pro23val (accessed [today's date]).

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