Is TECR p.Pro54Arg (c.161C>G) pathogenic?

TECR p.Pro54Arg (c.161C>G) is classified Uncertain significance in TECR (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-10-29). AlphaMissense: likely pathogenic (0.74); Very rare (popmax 0.0039%, nfe); Associated with intellectual disability, autosomal recessive 14.

What condition is associated with TECR p.Pro54Arg (c.161C>G)?

TECR p.Pro54Arg (c.161C>G) is associated with intellectual disability, autosomal recessive 14 (ClinVar).

How common is TECR p.Pro54Arg (c.161C>G) in the general population?

TECR p.Pro54Arg (c.161C>G) is very rare (popmax 0.0039%, nfe) (gnomAD).

What do computational predictors say about TECR p.Pro54Arg (c.161C>G)?

AlphaMissense predicts likely pathogenic (score 0.74) — an in-silico prediction, not a clinical call.

TECR p.Pro54Arg

c.161C>G · rs772297819 · VCV1029131

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely pathogenic

0.74 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.0039%, nfe)

Missense predictors

2/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

intellectual disability, autosomal recessive 14

Computational evidence

Protein change
AlphaMissense	0.74	likely pathogenic
REVEL	0.203	benign-leaning
SaProt	LLR -15.57	damaging
⇒ AlphaMissense and SaProt call this damaging; REVEL does not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.6	GERP 1.5, phastCons 1
Regional constraint	o/e 0.77	unconstrained · MANE · 36 kb · p 2.4e-06 · regional, not allelic
Overall
CADD	33.0	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0039% European (non-Finnish) · 46/1,179,914 alleles

Filtering AF 0.00299% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00267%

Overall 0.00291% 47/1,613,080 alleles · very rare exomes 44/1,460,920 · genomes 3/152,160 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0039%	25,650
African / African-American	0.00134%	74,906

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: TECR
Protein: p.Pro54Arg
Coding: c.161C>G
MANE Select: NM_138501
dbSNP: rs772297819
Type: single nucleotide variant
Location: chr19:14563700 (GRCh38)
Gene constraint: LOEUF 0.541 · pLI 0.85 (gnomAD)
Structure: AlphaFold pLDDT 94.45 · 1 PDB

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

Disease context

intellectual disability, autosomal recessive 14 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

TECR p.Val88Leu Uncertain significance ★★ ⚠ same condition
TECR c.16-15G>A Benign/Likely benign ★★ same condition
TECR p.Lys291= Likely benign ★★ same type
TECR p.Pro229= Likely benign ★★ same type
TECR p.Ser271= Benign/Likely benign ★★ same type
TECR p.Tyr184= Likely benign ★★ same type
TECR c.606+7A>C Uncertain significance ★ same type
TECR c.606+8G>A Uncertain significance ★ same type

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/tecr-p-pro54arg (accessed [today's date]).

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