Is TTC7A p.Ser294= (c.882C>T) pathogenic?

TTC7A p.Ser294= (c.882C>T) is classified Likely benign in TTC7A (ClinVar, Single submitter, 1 submitter; last evaluated 2018-11-13). Absent from gnomAD v4.1; Associated with multiple intestinal atresia.

What condition is associated with TTC7A p.Ser294= (c.882C>T)?

TTC7A p.Ser294= (c.882C>T) is associated with multiple intestinal atresia (ClinVar).

How common is TTC7A p.Ser294= (c.882C>T) in the general population?

TTC7A p.Ser294= (c.882C>T) is absent from gnomAD v4.1 (gnomAD).

TTC7A p.Ser294=

c.882C>T · rs1572846942 · VCV795237

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

multiple intestinal atresia

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 -2.7	GERP -4.3
Overall
CADD	5.574	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: TTC7A
Protein: p.Ser294=
Coding: c.882C>T
MANE Select: NM_020458
dbSNP: rs1572846942
Type: single nucleotide variant
Location: chr2:46994395 (GRCh38)
Gene constraint: LOEUF 1.198 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 84.59

Full TTC7A gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

multiple intestinal atresia — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

TTC7A p.Ser294Cys Uncertain significance ★ ⚠ same residue
TTC7A c.1288-1G>T Pathogenic/Likely pathogenic ★★ same condition
TTC7A c.1641+1G>A Likely pathogenic ★★ same condition
TTC7A c.2018-1G>C Pathogenic/Likely pathogenic ★★ same condition
TTC7A p.Arg138Ter Pathogenic/Likely pathogenic ★★ same condition
TTC7A p.Arg358Ter Pathogenic/Likely pathogenic ★★ same condition
TTC7A p.Arg405Ter Pathogenic/Likely pathogenic ★★ same condition
TTC7A p.Cys623Ter 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/ttc7a-p-ser294 (accessed [today's date]).

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