Is TCAP p.Ser31fs (c.90_91del) pathogenic?

TCAP p.Ser31fs (c.9091del) is classified Pathogenic/Likely pathogenic in TCAP (ClinVar, Multiple submitters, 4 submitters; last evaluated 2023-10-27). No gnomAD frequency available for this variant; Associated with Abnormality of the musculature.

What condition is associated with TCAP p.Ser31fs (c.90_91del)?

TCAP p.Ser31fs (c.90_91del) is associated with Abnormality of the musculature, autosomal recessive limb-girdle muscular dystrophy type 2G (ClinVar).

How common is TCAP p.Ser31fs (c.90_91del) in the general population?

TCAP p.Ser31fs (c.90_91del) is no gnomAD frequency available for this variant (gnomAD).

TCAP p.Ser31fs

c.90_91del · rs1555606976 · VCV446463

Pathogenic/Likely pathogenic Multiple submitters

Classification

Pathogenic/Likely pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

Abnormality of the musculature

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	escapes	premature termination codon within the last 50 nt of the penultimate exon (1 of 2, 21 nt from its 3' end) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 1.1	GERP 2.5, phastCons 0.53

Predicted loss-of-function is descriptive, not an applied PVS1 code.

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: TCAP
Protein: p.Ser31fs
Coding: c.90_91del
MANE Select: NM_003673
dbSNP: rs1555606976
Type: Deletion
Location: chr17:39665448 (GRCh38)
Gene constraint: LOEUF 1.374 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 79.89 · 2 PDB
Residue 31: a β-strand

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

Disease context

Abnormality of the musculature — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: autosomal recessive limb-girdle muscular dystrophy type 2G

Similar variants

TCAP c.110_110+1del Pathogenic ★★ same condition
TCAP c.110+1_110+5del Likely pathogenic ★ same condition
TCAP p.Gln56fs Likely pathogenic ★ same condition
TCAP p.Ser31Cys Uncertain significance ★ ⚠ same residue
TCAP p.Ser31Phe Uncertain significance ★ ⚠ same residue
TCAP p.Ser31Tyr Uncertain significance ★ ⚠ same residue
TCAP p.Ser31= Likely benign ★ same residue
TCAP c.110+5G>T 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/tcap-p-ser31fs (accessed [today's date]).

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