Is TTC7A p.Ser796= (c.2388C>T) pathogenic?

TTC7A p.Ser796= (c.2388C>T) is classified Likely benign in TTC7A (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-11-06). Very rare (popmax 0.00659%, sas); Associated with multiple intestinal atresia.

What condition is associated with TTC7A p.Ser796= (c.2388C>T)?

TTC7A p.Ser796= (c.2388C>T) is associated with multiple intestinal atresia (ClinVar).

How common is TTC7A p.Ser796= (c.2388C>T) in the general population?

TTC7A p.Ser796= (c.2388C>T) is very rare (popmax 0.00659%, sas) (gnomAD).

TTC7A p.Ser796=

c.2388C>T · rs370786690 · VCV1533918

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00659%, sas)

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 1.4	GERP 1.2, phastCons 1
Overall
CADD	9.77	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00659% South Asian · 6/91,086 alleles

Filtering AF 0.00326% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00294%

Overall 0.00372% 60/1,613,710 alleles · very rare exomes 58/1,461,472 · genomes 2/152,238 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00659%	15,181
European (non-Finnish)	0.00424%	23,601
Finnishnot grpmax-eligible	0.00314%	31,831
Remaining individualsnot grpmax-eligible	0.0016%	62,484
African / African-American	0.00133%	74,948

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: TTC7A
Protein: p.Ser796=
Coding: c.2388C>T
MANE Select: NM_020458
dbSNP: rs370786690
Type: single nucleotide variant
Location: chr2:47073734 (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.Ser796fs Likely pathogenic ★ same residue
TTC7A p.Ser796Asn 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

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-ser796 (accessed [today's date]).

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