Is TTC7A p.Arg34= (c.102G>C) pathogenic?

TTC7A p.Arg34= (c.102G>C) is classified Likely benign in TTC7A (ClinVar, Single submitter, 1 submitter; last evaluated 2026-01-27). Very rare (popmax 0.00273%, afr); Associated with multiple intestinal atresia.

What condition is associated with TTC7A p.Arg34= (c.102G>C)?

TTC7A p.Arg34= (c.102G>C) is associated with multiple intestinal atresia (ClinVar).

How common is TTC7A p.Arg34= (c.102G>C) in the general population?

TTC7A p.Arg34= (c.102G>C) is very rare (popmax 0.00273%, afr) (gnomAD).

TTC7A p.Arg34=

c.102G>C · rs1409686440 · VCV1109658

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00273%, afr)

Conditions

multiple intestinal atresia

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.238	benign-leaning
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 1.7	GERP -0.27, phastCons 1
Overall
CADD	12.12	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00273% African / African-American · 2/73,290 alleles

Filtering AF 0.00141% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00119%

Overall 0.00167% 26/1,553,094 alleles · very rare exomes 22/1,400,864 · genomes 4/152,230 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00273%	36,645
European (non-Finnish)	0.00209%	47,864

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.Arg34=
Coding: c.102G>C
MANE Select: NM_020458
dbSNP: rs1409686440
Type: single nucleotide variant
Location: chr2:46941643 (GRCh38)

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

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-arg34 (accessed [today's date]).

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